Methods for Detecting Receptor Complexes Comprising PDGFR

ABSTRACT

Abstract of the Disclosure 
      The invention is directed to a new class of biomarker in patient samples comprising dimers of ErbB cell surface membrane receptors.  In one aspect, the invention includes a method of determining the status of a disease or healthful condition by correlating such condition to amounts of one or more dimers of ErbB cell surface membrane receptors measured directly in a patient sample, in particular a fixed tissue sample.    In another aspect, the invention includes a method of determining a status of a cancer in a specimen from an individual by correlating measurements of amounts of one or more dimers of ErbB cell surface membrane receptors in cells of the specimen to such status, including presence or absence of a pre-cancerous state, presence or absence of a cancerous state, prognosis of a cancer, or responsiveness to treatment.  Preferably, methods of the invention are implemented by using sets of binding compounds having releasable molecular tags that are specific for multiple components of one or more types of receptor dimers.  After binding, molecular tags are released and separated from the assay mixture for analysis.

Detailed Description of the Invention Field of the Invention

The present invention relates generally to biomarkers, and moreparticularly, to the use of ErbB cell surface receptor complexes, suchas dimers and oligomers, as biomarkers.

Background of the Invention

A biomarker is a characteristic that is objectively measured andevaluated as an indicator of normal biological processes, pathogenicprocesses, or pharmacological responses to a therapeutic intervention,Atkinson et al, Clin. Pharmacol. Ther., 69: 89-95 (2001). Biomarkersvary widely in nature, ease of measurement, and correlation withphysiological states of interest, e.g. Frank et al, Nature Reviews DrugDiscovery, 2: 566-580 (2003). It is widely believed that the developmentof new validated biomarkers will lead both to significant reductions inhealthcare and drug development costs and to significant improvements intreatment for a wide variety of diseases and conditions. Thus, a greatdeal of effort has been directed to using new technologies to find newclasses of biomarkers, e.g. Petricoin et al, Nature Reviews DrugDiscovery, 1: 683-695 (2002); Sidransky, Nature Reviews Cancer, 2:210-219 (2002).

The interactions of cell surface membrane components play crucial rolesin transmitting extracellular signals to a cell in normal physiology,and in disease conditions. In particular, many types of cell surfacereceptors undergo dimerization, oligomerization, or clustering inconnection with the transduction of an extracellular event or signal,e.g. ligand-receptor binding, into a cellular response, such asproliferation, increased or decreased gene expression, or the like, e.g.George et al, Nature Reviews Drug Discovery, 1: 808-820 (2002); Melladoet al, Ann. Rev. Immunol., 19: 397-421 (2001); Schlessinger, Cell, 103:211-225 (2000); Yarden, Eur. J. Cancer, 37: S3-S8 (2001). The role ofsuch signal transduction events in diseases, such as cancer, has beenthe object of intense research and has led to the development of severalnew drugs and drug candidates, e.g. Herbst and Shin, Cancer, 94:1593-1611 (2002); Yarden and Sliwkowski, Nature Reviews Molecular CellBiology, 2: 127-137 (2001); McCormick, Trends in Cell Biology, 9: 53-56(1999); Blume-Jensen and Hunter, Nature, 411: 355-365 (2001).

Expression levels of individual cell surface receptors have been usedsuccessfully as biomarkers, e.g. Slamon et al, U.S. patent 4,968,603(Her2 expression). However, individual receptor expression level aloneis not always a reliable indicator of a disease status or condition,e.g. Chow et al, Clin. Cancer Res., 7: 1957-1962 (2001) (EGFR, or Her1,expression). Despite the important role that receptor dimerization playsin cellular and disease processes, receptor dimer expression has notbeen employed as a biomarker, in part due to the inconvenience and lackof sensitivity of current measurement technologies and the inability orimpracticality of using such technologies to carry out measurements onpatient samples, which may be formalin fixed and/or in too small aquantity for analysis, e.g. Price et al, Methods in Molecular Biology,218: 255-267 (2003); Stagljar, Science STKE 2003, pe56 (2003); Koll etal, International patent publication WO 2004/008099; Golemis, editor,Protein-Protein Interactions (Cold Spring Harbor Laboratory Press, NewYork, 2002); Sorkin et al, Curr. Biol., 10: 1395-1398 (2000); McVey etal, J. Biol. Chem., 17: 14092-14099 (2001); Salim et al, J. Biol. Chem.,277: 15482-15485 (2002); Angers et al, Annu. Rev. Pharmacol. Toxicol.,42: 409-435 (2002); Szollosi et al, Reviews in Molecular Biotechnology,82: 251-266 (2002); Matko et al, Meth. in Enzymol., 278: 444-462 (1997);Reed-Gitomer, U.S. Patent 5,192,660.

In view of the above, the availability of a new class of biomarkers inpatient samples based on the presence, absence, and/or profile or ratiosof cell surface receptor dimers or complexes involved with keyintracellular processes, such as signal transduction, would advance thefield of medicine by providing a new tool for diagnosis, prognosis,patient stratification, and drug development.

SUMMARY OF THE INVENTION

The invention is directed to biomarkers comprising ErbB receptorcomplexes in cell surface membranes of patient cell or tissue samples,particularly samples preserved by conventional procedures, such asfreezing or fixation. In one aspect, the invention includes a method ofdetermining the status of a disease or healthful condition bycorrelating such condition to amounts of one or more ErbB receptorcomplexes in cell surface membranes in a cell or tissue sample from anindividual. In another aspect, the invention includes a method ofdetermining a status of a cancer in a specimen from an individual bycorrelating measurements of amounts of one or more ErbB surface receptorcomplexes in the specimen to such status. The invention additionallyprovides a method of predicting the effectiveness of ErbB-dimer-actingdrugs, for example, in cancer therapy, by relating numbers and types ofdrug-responsive ErbB dimers to efficacy, or a likelihood of patientresponsiveness.

In one aspect, the invention permits the determination of a diseasestatus of a patient suffering from a disease characterized by aberrantexpression of one or more ErbB cell surface receptor complexes by thefollowing steps: (i) measuring an amount of each of one or more ErbBcell surface receptor complexes in a patient sample; (ii) comparing eachsuch amount to its corresponding amount in a reference sample; and (iii)correlating differences in the amounts from the patient sample and therespective corresponding amounts from the reference sample to thedisease status the patient. A patient sample may be fixed or frozen;however, preferably, a patient sample is fixed using conventionalprotocols.

In a particular aspect, the invention provides a method of determiningfrom measurements on patient samples, especially fixed samples, thedisease status of a patient suffering from a cancer, wherein suchmeasurement are of the types and/or amounts of ErbB receptor complexes,which are also referred to herein as “Her receptor complexes.” Suchreceptor complexes include, but are not limited to, one or more ofHer1-Her1 homodimers, Her2-Her2 homodimers, Her1-Her2 receptor dimers,Her2-Her3 receptor dimers, Her1-Her3 receptor dimers, Her2-Her4 receptordimers, Her1-PI3K complexes, Her2-PI3K complexes, Her3-PI3K complexes,Her1-SHC complexes, Her2-SHC complexes, Her3-SHC complexes, Her1-IGF-1Rreceptor dimers, Her2-IGF-1R receptor dimers, Her3-IGF-1R receptordimers, Her1-PDGFR receptor dimers, Her2-PDGFR receptor dimers,Her3-PDGFR receptor dimers, p95Her2-Her3 receptor dimers, p95Her2-Her2receptor dimers, p95Her2-Her1 receptor dimers, EGFRvIII-Her1 receptordimers, EGFRvIII-Her2 receptor dimers, and EGFRvIII-Her3 receptordimers. In other embodiments, such Her receptor complexes are selectedfrom the group consisting of Her1-Her2 receptor dimers and Her2-Her3receptor dimers; or the group consisting of Her1-Her2 receptor dimers,Her2-Her3 receptor dimers, and Her1-Her3 receptor dimers. In anotherembodiment, the invention includes measurement of complexes comprising aHer receptor and an intracellular adaptor molecule, particularly,intracellular adaptor molecules that form complexes with a Her receptorin response to phosphorylation of such receptor. Exemplary receptorcomplexes of Her receptors and intracellular adaptor molecules includecomplexes selected from the group consisting of Her1-PI3K complexes,Her2-PI3K complexes, Her3-PI3K complexes, Her1-SHC complexes, Her2-SHCcomplexes, and Her3-SHC complexes. The invention further includes theassociation of receptor heterodimers comprising a Her receptor andanother receptor tyrosine kinase to a disease status. Exemplary receptorcomplexes of Her receptors and other receptor tyrosine kinases includereceptor complexes selected from the group consisting of Her1-IGF-1Rreceptor dimers, Her2-IGF-1R receptor dimers, Her3-IGF-1R receptordimers, Her1-PDGFR receptor dimers, Her2-PDGFR receptor dimers, andHer3-PDGFR receptor dimers. The invention further includes theassociation of receptor dimers comprising a full-length Her receptor anda truncated Her receptor to a disease status. Exemplary receptorcomplexes of full-length Her receptors and truncated Her receptorsinclude receptor complexes selected from group consisting ofp95Her2-Her3 receptor dimers, EGFRvIII-Her1 receptor dimers,EGFRvIII-Her2 receptor dimers, and EGFRvIII-Her3 receptor dimers. Inanother aspect, such method of determining disease status includesdetermining the effectiveness of, or the responsiveness of a patient to,dimer-acting drugs for treating cancer, the dimer-acting drug acting onHer receptor complexes as described above.

In another aspect the invention includes improved determinations of adisease status by measuring expression of Her1-Her3 receptor complexesin a patient sample, as well as expression of Her1-Her2 and Her2-Her3receptor complexes.

In another aspect, the invention provides a method of determining astatus of a cancer in a patient by determining amounts of one or moredimers of ErbB cell surface membrane receptors or relative amounts of aplurality of dimers of cell surface membrane receptors in a cell ortissue sample from such patient. In one embodiment, such dimers aremeasured using at least two reagents, referred to herein as reagentpairs, that are specific for different members of each dimer: onereagent, referred to herein as a cleaving probe, has a cleavage-inducingmoiety that may be induced to cleave susceptible bonds within itsimmediate proximity; and the other reagent, referred to herein as abinding compound, has one or more molecular tags attach by linkages thatare cleavable by the cleavage-inducing moiety. In accordance with theembodiment, whenever such different members form a dimer, the cleavablelinkages are brought within the effective cleaving proximity of thecleavage-inducing moiety so that molecular tags are released. Thereleased molecular tags are then separated from the reaction mixture andquantified to provide a measure of dimer formation.

In another aspect of the invention, ErbB receptor dimers in a patientsample are measured ratiometrically; that is, the amount of an ErbBdimer is given as a ratio of a measure of one component present in thedimer to a measure of the total amount of the other component of thedimer, whether it is present in the dimer or in monomeric form. In oneembodiment, typical measures include peak height or peak area of peaksin an electropherogram that are correlated to particular molecular tags.

In a particular embodiment of this aspect, the invention provides amethod of determining a status of a cancer in a patient bysimultaneously determining amounts of a plurality of Her receptor dimersin a fixed tissue sample from the patient. Such dimers may be measuredusing at least two reagents that are specific for different members ofeach dimer: one reagent, referred to herein as a cleaving probe, has acleavage-inducing moiety that may be induced to cleave susceptible bondswithin its immediate proximity; and the other reagent, referred toherein as a binding compound, has one or more molecular tags attach bylinkages that are cleavable by the cleavage-inducing moiety. Inaccordance with the embodiment, whenever Her receptor dimers form, thecleavable linkages of the binding compounds are brought within theeffective cleaving proximity of the cleavage-inducing moiety so thatmolecular tags are released. The molecular tags are then separated fromthe reaction mixture and quantified to provide a measure of Her receptordimer populations. In another embodiment of this aspect, relativeamounts of a plurality of Her receptor dimers are measured and relatedto a status of a cancer in a patient. Exemplary cancers include, but arenot limited to, breast cancer, ovarian cancer, and prostate cancer.Exemplary Her receptor dimers include, but are not limited to, Her1-Her2receptor dimers, Her1-Her3 receptor dimers, Her2-Her3 receptor dimers,and Her2-Her4 receptor dimers, as well as those listed above.

The present invention provides biomarkers comprising measures of theamounts of ErbB receptor complexes in patient samples. In particular,profiles of ErbB receptor complex populations may be correlated todisease status of a patient, and in some embodiments, to prognosis,efficacy of ErbB dimer-acting drugs, and likelihood of patientresponsiveness to therapy. In accordance with the invention, shortcomings in the art are overcome by enabling the direct measurement ofErbB receptor complexes in patient samples without the need to cultureor otherwise process the cell or tissue samples by methodologies, suchas xenografting, that increase cost and labor as well as introducingsources of noise and potential artifacts into the final assay readouts.The present invention also provides a surrogate measurement forintracellular receptor phosphorylation, or other modifications that areeasily destroyed in sample preparation procedures. Such surrogatemeasurements are based on the measurement of complexes, such as PI3K orSHC-receptor complexes, and the like, that depend on the abovemodifications for their formation and that are less affected by samplepreparation procedures.

BRIEF DESCRIPTION OF THE DRAWINGS

Figures 1A-1F illustrate diagrammatically the use of releasablemolecular tags to measure receptor dimer populations.

Figures 1G-1H illustrate diagrammatically the use of releasablemolecular tags to measure cell surface receptor complexes in fixedtissue specimens.

Figures 2A-2E illustrate diagrammatically an embodiment of the method ofthe invention for profiling relative amounts of dimers of a plurality ofreceptor types.

Figures 3A-3D illustrate diagrammatically methods for attachingmolecular tags to antibodies.

Figures 4A-4E illustrate data from assays on SKBR-3 and BT-20 celllysates for receptor heterodimers using a method of the invention.

Figures 5A-5C illustrate data from assays for receptor heterodimers onhuman normal and tumor breast tissue samples using a method of theinvention.

Figures 6A and 6B illustrate data from assays of the invention fordetecting homodimers and phosphorylation of Her1 in lysates of BT-20cells.

Figure 7 shows data from assays of the invention that show Her2homodimer populations on MCF-7 and SKBR-3 cell lines.

Figures 8A-8B show data from assays of the invention that detectheterodimers of Her1 and Her3 on cells in response to increasingconcentrations of heregulin (HRG).

Figures 9A and 9B show data on the increases in the numbers of Her1-Her3heterodimers on 22Rv1 and A549 cells, respectively, with increasingconcentrations of epidermal growth factor (EGF).

Figures 10A-10C show data on the expression of heterodimers of IGF-1Rand various Her receptors in frozen samples from human breast tissue.

Figures 11A-11D illustrate the assay design and experimental results fordetecting a PI3 kinase-Her3 receptor activation complex.

Figures 12A-12D illustrate the assay design and experimental results fordetecting a Shc/Her3 receptor-adaptor complex.

Fig. 13 shows data for a correlation between expression of Her2-Her3heterodimers and PI3K//Her3 complexes in tumor cells.

Figs. 14A-14B show measurements of Her1-Her2 and Her2-Her3 receptordimer populations obtained from normal breast tissue samples and frombreast tumor tissue samples.

Figs. 15A-15G show measurements of Her1-Her1 and Her2-Her2 homodimersand Her1-Her2 and Her2-Her3 heterodimers in sections of fixed pellets ofcancer cell lines.

Definitions

“Antibody” means an immunoglobulin that specifically binds to, and isthereby defined as complementary with, a particular spatial and polarorganization of another molecule. The antibody can be monoclonal orpolyclonal and can be prepared by techniques that are well known in theart such as immunization of a host and collection of sera (polyclonal)or by preparing continuous hybrid cell lines and collecting the secretedprotein (monoclonal), or by cloning and expressing nucleotide sequencesor mutagenized versions thereof coding at least for the amino acidsequences required for specific binding of natural antibodies.Antibodies may include a complete immunoglobulin or fragment thereof,which immunoglobulins include the various classes and isotypes, such asIgA, IgD, IgE, IgG1, IgG2a, IgG2b and IgG3, IgM, etc. Fragments thereofmay include Fab, Fv and F(ab’)2, Fab’, and the like. In addition,aggregates, polymers, and conjugates of immunoglobulins or theirfragments can be used where appropriate so long as binding affinity fora particular polypeptide is maintained. Guidance in the production andselection of antibodies for use in immunoassays, including such assaysemploying releasable molecular tag (as described below) can be found inreadily available texts and manuals, e.g. Harlow and Lane, Antibodies: ALaboratory Manual (Cold Spring Harbor Laboratory Press, New York, 1988);Howard and Bethell, Basic Methods in Antibody Production andCharacterization (CRC Press, 2001); Wild, editor, The ImmunoassayHandbook (Stockton Press, New York, 1994), and the like.

“Antibody binding composition” means a molecule or a complex ofmolecules that comprises one or more antibodies, or fragments thereof,and derives its binding specificity from such antibody or antibodyfragment. Antibody binding compositions include, but are not limited to,(i) antibody pairs in which a first antibody binds specifically to atarget molecule and a second antibody binds specifically to a constantregion of the first antibody; a biotinylated antibody that bindsspecifically to a target molecule and a streptavidin protein, whichprotein is derivatized with moieties such as molecular tags orphotosensitizers, or the like, via a biotin moiety; (ii) antibodiesspecific for a target molecule and conjugated to a polymer, such asdextran, which, in turn, is derivatized with moieties such as moleculartags or photosensitizers, either directly by covalent bonds orindirectly via streptavidin-biotin linkages; (iii) antibodies specificfor a target molecule and conjugated to a bead, or microbead, or othersolid phase support, which, in turn, is derivatized either directly orindirectly with moieties such as molecular tags or photosensitizers, orpolymers containing the latter.

“Antigenic determinant,” or “epitope” means a site on the surface of amolecule, usually a protein, to which a single antibody molecule binds;generally a protein has several or many different antigenic determinantsand reacts with antibodies of many different specificities. A preferredantigenic determinant is a phosphorylation site of a protein.

“Binding moiety” means any molecule to which molecular tags can bedirectly or indirectly attached that is capable of specifically bindingto an analyte. Binding moieties include, but are not limited to,antibodies, antibody binding compositions, peptides, proteins, nucleicacids, and organic molecules having a molecular weight of up to 1000daltons and consisting of atoms selected from the group consisting ofhydrogen, carbon, oxygen, nitrogen, sulfur, and phosphorus. Preferably,binding moieties are antibodies or antibody binding compositions.

“Cancer” and "cancerous" refer to or describe the physiologicalcondition in mammals that is typically characterized by unregulated cellgrowth. Examples of cancer include, but are not limited to, carcinoma,lymphoma, blastoma, sarcoma, and leukemia. More particular examples ofsuch cancers include squamous cell cancer, small-cell lung cancer,non-small cell lung cancer, gastrointestinal cancer, pancreatic cancer,glioblastoma, cervical cancer, ovarian cancer, liver cancer, bladdercancer, hepatoma, breast cancer, colon cancer, colorectal cancer,endometrial carcinoma, salivary gland carcinoma, kidney cancer, prostatecancer, vulval cancer, thyroid cancer, hepatic carcinoma and varioustypes of head and neck cancer.

“Complex” as used herein means an assemblage or aggregate of moleculesin direct or indirect contact with one another. In one aspect,“contact,” or more particularly, “direct contact” in reference to acomplex of molecules, or in reference to specificity or specificbinding, means two or more molecules are close enough so that attractivenoncovalent interactions, such as Van der Waal forces, hydrogen bonding,ionic and hydrophobic interactions, and the like, dominate theinteraction of the molecules. In such an aspect, a complex of moleculesis stable in that under assay conditions the complex isthermodynamically more favorable than a non-aggregated, ornon-complexed, state of its component molecules. As used herein,“complex” usually refers to a stable aggregate of two or more proteins,and is equivalently referred to as a “protein-protein complex.” Mosttypically, a “complex” refers to a stable aggregate of two proteins.

“Dimer” in reference to cell surface membrane receptors means a complexof two or more membrane-bound receptor proteins that may be the same ordifferent. Dimers of identical receptors are referred to as “homodimers”and dimers of different receptors are referred to as “heterodimers.”Dimers usually consist of two receptors in contact with one another.Dimers may be created in a cell surface membrane by passive processes,such as Van der Waal interactions, and the like, as described above inthe definition of “complex,” or dimers may be created by activeprocesses, such as by ligand-induced dimerization, covalent linkages,interaction with intracellular components, or the like, e.g.Schlessinger, Cell, 103: 211-225 (2000). As used herein, the term“dimer” is understood to refer to “cell surface membrane receptordimer,” unless understood otherwise from the context.

“Disease status” includes, but is not limited to, the followingfeatures: likelihood of contracting a disease, presence or absence of adisease, prognosis of disease severity, and likelihood that a patientwill respond to treatment by a particular therapeutic agent that actsthrough a receptor complex. In regard to cancer, “disease status”further includes detection of precancerous or cancerous cells ortissues, the selection of patients that are likely to respond totreatment by a therapeutic agent that acts through one or more receptorcomplexes, such as one or more receptor dimers, and the ameliorativeeffects of treatment with such therapeutic agents. In one aspect,disease status in reference to Her receptor complexes means likelihoodthat a cancer patient will respond to treatment by a Her, or ErbB,dimer-acting drug. Preferably, such cancer patient is a breast orovarian cancer patient and such Her dimer-acting drugs include Omnitarg(2C4), Herceptin, ZD-1839 (Iressa), and OSI-774 (Tarceva).

"ErbB receptor" or “Her receptor” is a receptor protein tyrosine kinasewhich belongs to the ErbB receptor family and includes EGFR (“Her1”),ErbB2 (“Her2”), ErbB3 (“Her3”) and ErbB4 (“Her4”) receptors. The ErbBreceptor generally comprises an extracellular domain, which may bind anErbB ligand; a lipophilic transmembrane domain; a conservedintracellular tyrosine kinase domain; and a carboxyl-terminal signalingdomain harboring several tyrosine residues which can be phosphorylated.The ErbB receptor may be a native sequence ErbB receptor or an aminoacid sequence variant thereof. Preferably the ErbB receptor is nativesequence human ErbB receptor. In one aspect, ErbB receptor includestruncated versions of Her receptors, including but not limited to,EGFRvIII and p95Her2, disclosed in Chu et al, Biochem. J., 324: 855-861(1997); Xia et al, Oncogene, 23: 646-653 (2004); and the like.

The terms "ErbB1", "epidermal growth factor receptor" and "EGFR" and“Her1” are used interchangeably herein and refer to native sequence EGFRas disclosed, for example, in Carpenter et al. Ann. Rev. Biochem.56:881-914 (1987), including variants thereof (e.g. a deletion mutantEGFR as in Humphrey et al. PNAS (USA) 87:4207-4211 (1990)). erbB1 refersto the gene encoding the EGFR protein product. Examples of antibodieswhich bind to EGFR include MAb 579 (ATCC CRL RB 8506), MAb 455 (ATCC CRLHB8507), MAb 225 (ATCC CRL 8508), MAb 528 (ATCC CRL 8509) (see, U.S.Pat. No. 4,943,533, Mendelsohn et al.) and variants thereof, such aschimerized 225 (C225) and reshaped human 225 (H225) (see, WO 96/40210,Imclone Systems Inc.).

"Her2", "ErbB2" "c-Erb-B2" are used interchangeably. Unless indicatedotherwise, the terms "ErbB2" "c-Erb-B2" and "Her2" when used hereinrefer to the human protein. The human ErbB2 gene and ErbB2 protein are,for example, described in Semba et al., PNAS (USA) 82:6497-650 (1985)andYamamoto et al. Nature 319:230-234 (1986) (Genebank accession numberX03363). Examples of antibodies that specifically bind to Her2 aredisclosed in U.S. patents 5,677,171; 5,772,997; Fendly et al, CancerRes., 50: 1550-1558 (1990); and the like.

"ErbB3" and"Her3" refer to the receptor polypeptide as disclosed, forexample, in U.S. Pat. Nos. 5,183,884 and 5,480,968 as well as Kraus etal. PNAS (USA) 86:9193-9197 (1989), including variants thereof. Examplesof antibodies which bind Her3 are described in U.S. Pat. No. 5,968,511,e.g. the 8B8 antibody (ATCC HB 12070).

The terms "ErbB4" and "Her4" herein refer to the receptor polypeptide asdisclosed, for example, in EP Pat Appln No 599,274; Plowman et al.,Proc. Natl. Acad. Sci. USA, 90:1746-1750 (1993); and Plowman et al.,Nature, 366:473-475 (1993), including variants thereof such as the Her4isoforms disclosed in WO 99/19488.

“Insulin-like growth factor-1 receptor” or “IGF-1R” means a humanreceptor tyrosine kinase substantially identical to those disclosed inUllrich et al, EMBO J., 5: 2503-2512 (1986) or Steele-Perkins et al, J.Biol. Chem., 263: 11486-11492 (1988).

“Isolated” in reference to a polypeptide or protein means substantiallyseparated from the components of its natural environment. Preferably, anisolated polypeptide or protein is a composition that consists of atleast eighty percent of the polypeptide or protein identified bysequence on a weight basis as compared to components of its naturalenvironment; more preferably, such composition consists of at leastninety-five percent of the polypeptide or protein identified by sequenceon a weight basis as compared to components of its natural environment;and still more preferably, such composition consists of at leastninety-nine percent of the polypeptide or protein identified by sequenceon a weight basis as compared to components of its natural environment.Most preferably, an isolated polypeptide or protein is a homogeneouscomposition that can be resolved as a single spot after conventionalseparation by two-dimensional gel electrophoresis based on molecularweight and isoelectric point. Protocols for such analysis byconventional two-dimensional gel electrophoresis are well known to oneof ordinary skill in the art, e.g. Hames and Rickwood, Editors, GelElectrophoresis of Proteins: A Practical Approach (IRL Press, Oxford,1981); Scopes, Protein Purification (Springer-Verlag, New York, 1982);Rabilloud, Editor, Proteome Research: Two-Dimensional GelElectrophoresis and Identification Methods (Springer-Verlag, Berlin,2000).

“Kit” refers to any delivery system for delivering materials or reagentsfor carrying out a method of the invention. In the context of reactionassays, such delivery systems include systems that allow for thestorage, transport, or delivery of reaction reagents (e.g., probes,enzymes, etc. in the appropriate containers) and/or supporting materials(e.g., buffers, written instructions for performing the assay etc.) fromone location to another. For example, kits include one or moreenclosures (e.g., boxes) containing the relevant reaction reagentsand/or supporting materials. Such contents may be delivered to theintended recipient together or separately. For example, a firstcontainer may contain an enzyme for use in an assay, while a secondcontainer contains probes.

“Percent identical,” or like term, used in respect of the comparison ofa reference sequence and another sequence (i.e. a “candidate” sequence)means that in an optimal alignment between the two sequences, thecandidate sequence is identical to the reference sequence in a number ofsubunit positions equivalent to the indicated percentage, the subunitsbeing nucleotides for polynucleotide comparisons or amino acids forpolypeptide comparisons. As used herein, an “optimal alignment” ofsequences being compared is one that maximizes matches between subunitsand minimizes the number of gaps employed in constructing an alignment.Percent identities may be determined with commercially availableimplementations of algorithms described by Needleman and Wunsch, J. Mol.Biol., 48: 443-453 (1970)(“GAP” program of Wisconsin Sequence AnalysisPackage, Genetics Computer Group, Madison, WI). Other software packagesin the art for constructing alignments and calculating percentageidentity or other measures of similarity include the “BestFit” program,based on the algorithm of Smith and Waterman, Advances in AppliedMathematics, 2: 482-489 (1981) (Wisconsin Sequence Analysis Package,Genetics Computer Group, Madison, WI). In other words, for example, toobtain a polypeptide having an amino acid sequence at least 95 percentidentical to a reference amino acid sequence, up to five percent of theamino acid residues in the reference sequence many be deleted orsubstituted with another amino acid, or a number of amino acids up tofive percent of the total amino acid residues in the reference sequencemay be inserted into the reference sequence. These alterations of thereference sequence many occur at the amino or carboxy terminal positionsof the reference amino acid sequence or anywhere between those terminalpositions, interspersed either individually among residues in thereference sequence of in one or more contiguous groups with in thereferences sequence. It is understood that in making comparisons withreference sequences of the invention that candidate sequence may be acomponent or segment of a larger polypeptide or polynucleotide and thatsuch comparisons for the purpose computing percentage identity is to becarried out with respect to the relevant component or segment.

“Phosphatidylinositol 3 kinase protein,” or equivalently a “PI3Kprotein,” means a human intracellular protein of the set of humanproteins describe under NCBI accession numbers NP_852664, NP_852556, andNP_852665, and proteins having amino acid sequences substantiallyidentical thereto.

“Platelet-derived growth factor receptor” or “PDGFR” means a humanreceptor tyrosine kinase protein that is substantially identical toPDGFR alpha or PDGFR beta, or variants thereof, described in Heldin etal, Physiological Reviews, 79: 1283-1316 (1999). In one aspect, theinvention includes determining the status of cancers, pre-cancerousconditions, fibrotic or sclerotic conditions by measuring one or moredimers of the following group: PDGFR alpha homodimers, PDGFR betahomodimers, and PDGFR alpha- PDGFR beta heterodimers. In particular,fibrotic conditions include lung or kidney fibrosis, and scleroticconditions include atherosclerosis. Cancers include, but are not limitedto, breast cancer, colorectal carcinoma, glioblastoma, and ovariancarcinoma. Reference to “PDGFR” alone is understood to mean “PDGFRalpha” or “PDGFR beta.”

“Polypeptide” refers to a class of compounds composed of amino acidresidues chemically bonded together by amide linkages with eliminationof water between the carboxy group of one amino acid and the amino groupof another amino acid. A polypeptide is a polymer of amino acidresidues, which may contain a large number of such residues. Peptidesare similar to polypeptides, except that, generally, they are comprisedof a lesser number of amino acids. Peptides are sometimes referred to asoligopeptides. There is no clear-cut distinction between polypeptidesand peptides. For convenience, in this disclosure and claims, the term“polypeptide” will be used to refer generally to peptides andpolypeptides. The amino acid residues may be natural or synthetic.

“Protein” refers to a polypeptide, usually synthesized by a biologicalcell, folded into a defined three-dimensional structure. Proteins aregenerally from about 5,000 to about 5,000,000 or more in molecularweight, more usually from about 5,000 to about 1,000,000 molecularweight, and may include posttranslational modifications, suchacetylation, acylation, ADP-ribosylation, amidation, covalent attachmentof flavin, covalent attachment of a heme moiety, covalent attachment ofa nucleotide or nucleotide derivative, covalent attachment of a lipid orlipid derivative, covalent attachment of phosphotidylinositol,cross-linking, cyclization, disulfide bond formation, farnesylation,demethylation, formation of covalent cross-links, formation of cystine,formation of pyroglutamate, formylation, gamma-carboxylation,glycosylation, GPI anchor formation, hydroxylation, iodination,methylation, myristoylation, oxidation, phosphorylation, prenylation,racemization, selenoylation, sulfation, and ubiquitination, e.g. Wold,F., Post-translational Protein Modifications: Perspectives andProspects, pgs. 1-12 in Post-translational Covalent Modification ofProteins, B. C. Johnson, Ed., Academic Press, New York, 1983. Proteinsinclude, by way of illustration and not limitation, cytokines orinterleukins, enzymes such as, e.g., kinases, proteases, galactosidasesand so forth, protamines, histones, albumins, immunoglobulins,scleroproteins, phosphoproteins, mucoproteins, chromoproteins,lipoproteins, nucleoproteins, glycoproteins, T-cell receptors,proteoglycans, and the like.

“Reference sample” means one or more cell, xenograft, or tissue samplesthat are representative of a normal or non-diseased state to whichmeasurements on patient samples are compared to determine whether areceptor complex is present in excess or is present in reduced amount inthe patient sample. The nature of the reference sample is a matter ofdesign choice for a particular assay and may be derived or determinedfrom normal tissue of the patient him- or herself, or from tissues froma population of healthy individuals. Preferably, values relating toamounts of receptor complexes in reference samples are obtained underessentially identical experimental conditions as corresponding valuesfor patient samples being tested. Reference samples may be from the samekind of tissue as that the patient sample, or it may be from differenttissue types, and the population from which reference samples areobtained may be selected for characteristics that match those of thepatient, such as age, sex, race, and the like. Typically, in assays ofthe invention, amounts of receptor complexes on patient samples arecompared to corresponding values of reference samples that have beenpreviously tabulated and are provided as average ranges, average valueswith standard deviations, or like representations.

“Receptor complex” means a complex that comprises at least one cellsurface membrane receptor. Receptor complexes may include a dimer ofcell surface membrane receptors, or one or more intracellular proteins,such as adaptor proteins, that form links in the various signalingpathways. Exemplary intracellular proteins that may be part of areceptor complex includes, but is not limit to, PI3K proteins, Grb2proteins, Grb7 proteins, Shc proteins, and Sos proteins, Src proteins,Cbl proteins, PLC gamma proteins, Shp2 proteins, GAP proteins, Nckproteins, Vav proteins, and Crk proteins. In one aspect, receptorcomplexes include PI3K or Shc proteins.

“Receptor tyrosine kinase,” or “RTK,” means a human receptor proteinhaving intracellular kinase activity and being selected from the RTKfamily of proteins described in Schlessinger, Cell, 103: 211-225 (2000);and Blume-Jensen and Hunter (cited above). “Receptor tyrosine kinasedimer” means a complex in a cell surface membrane comprising tworeceptor tyrosine kinase proteins. In some aspects, a receptor tyrosinekinase dimer may comprise two covalently linked receptor tyrosine kinaseproteins. Exemplary RTK dimers are listed in Table I. RTK dimers ofparticular interest are Her receptor dimers and VEGFR dimers.

“Sample” or “tissue sample" or “patient sample” or “patient cell ortissue sample” or “specimen” each means a collection of similar cellsobtained from a tissue of a subject or patient. The source of the tissuesample may be solid tissue as from a fresh, frozen and/or preservedorgan or tissue sample or biopsy or aspirate; blood or any bloodconstituents; bodily fluids such as cerebral spinal fluid, amnioticfluid, peritoneal fluid, or interstitial fluid; or cells from any timein gestation or development of the subject. The tissue sample maycontain compounds which are not naturally intermixed with the tissue innature such as preservatives, anticoagulants, buffers, fixatives,nutrients, antibiotics, or the like. In one aspect of the invention,tissue samples or patient samples are fixed, particularly conventionalformalin-fixed paraffin-embedded samples. Such samples are typicallyused in an assay for receptor complexes in the form of thin sections,e.g. 3-10 um thick, of fixed tissue mounted on a microscope slide, orequivalent surface. Such samples also typically undergo a conventionalre-hydration procedure, and optionally, an antigen retrieval procedureas a part of, or preliminary to, assay measurements.

“Separation profile” in reference to the separation of molecular tagsmeans a chart, graph, curve, bar graph, or other representation ofsignal intensity data versus a parameter related to the molecular tags,such as retention time, mass, or the like, that provides a readout, ormeasure, of the number of molecular tags of each type produced in anassay. A separation profile may be an electropherogram, a chromatogram,an electrochromatogram, a mass spectrogram, or like graphicalrepresentation of data depending on the separation technique employed. A“peak” or a “band” or a “zone” in reference to a separation profilemeans a region where a separated compound is concentrated. There may bemultiple separation profiles for a single assay if, for example,different molecular tags have different fluorescent labels havingdistinct emission spectra and data is collected and recorded at multiplewavelengths. In one aspect, released molecular tags are separated bydifferences in electrophoretic mobility to form an electropherogramwherein different molecular tags correspond to distinct peaks on theelectropherogram. A measure of the distinctness, or lack of overlap, ofadjacent peaks in an electropherogram is “electrophoretic resolution,”which may be taken as the distance between adjacent peak maximumsdivided by four times the larger of the two standard deviations of thepeaks. Preferably, adjacent peaks have a resolution of at least 1.0, andmore preferably, at least 1.5, and most preferably, at least 2.0. In agiven separation and detection system, the desired resolution may beobtained by selecting a plurality of molecular tags whose members haveelectrophoretic mobilities that differ by at least a peak-resolvingamount, such quantity depending on several factors well known to thoseof ordinary skill, including signal detection system, nature of thefluorescent moieties, the diffusion coefficients of the tags, thepresence or absence of sieving matrices, nature of the electrophoreticapparatus, e.g. presence or absence of channels, length of separationchannels, and the like. Electropherograms may be analyzed to associatefeatures in the data with the presence, absence, or quantities ofmolecular tags using analysis programs, such as disclosed in Williams etal, U.S. patent publication 2003/0170734 A1.

“SHC” (standing for “Src homology 2/ alpha-collagen-related”) means anyone of a family of adaptor proteins (66, 52, and 46 kDalton) in RTKsignaling pathways substantially identical to those described in Pelicciet al, Cell, 70: 93-104 (1992). In one aspect, SHC means the humanversions of such adaptor proteins.

“Signaling pathway” or “signal transduction pathway” means a series ofmolecular events usually beginning with the interaction of cell surfacereceptor with an extracellular ligand or with the binding of anintracellular molecule to a phosphorylated site of a cell surfacereceptor that triggers a series of molecular interactions, wherein theseries of molecular interactions results in a regulation of geneexpression in the nucleus of a cell. “Ras-MAPK pathway” means asignaling pathway that includes the phosphorylation of a MAPK proteinsubsequent to the formation of a Ras-GTP complex. “PI3K-Akt pathway”means a signaling pathway that includes the phosphorylation of an Aktprotein by a PI3K protein.

“Specific” or “specificity” in reference to the binding of one moleculeto another molecule, such as a binding compound, or probe, for a targetanalyte or complex, means the recognition, contact, and formation of astable complex between the probe and target, together with substantiallyless recognition, contact, or complex formation of the probe with othermolecules. In one aspect, “specific” in reference to the binding of afirst molecule to a second molecule means that to the extent the firstmolecule recognizes and forms a complex with another molecules in areaction or sample, it forms the largest number of the complexes withthe second molecule. In one aspect, this largest number is at leastfifty percent of all such complexes form by the first molecule.Generally, molecules involved in a specific binding event have areas ontheir surfaces or in cavities giving rise to specific recognitionbetween the molecules binding to each other. Examples of specificbinding include antibody-antigen interactions, enzyme-substrateinteractions, formation of duplexes or triplexes among polynucleotidesand/or oligonucleotides, receptor-ligand interactions, and the like.

“Spectrally resolvable” in reference to a plurality of fluorescentlabels means that the fluorescent emission bands of the labels aresufficiently distinct, i.e. sufficiently non-overlapping, that moleculartags to which the respective labels are attached can be distinguished onthe basis of the fluorescent signal generated by the respective labelsby standard photodetection systems, e.g. employing a system of band passfilters and photomultiplier tubes, or the like, as exemplified by thesystems described in U.S. Pat. Nos. 4,230,558; 4,811,218, or the like,or in Wheeless et al, pgs. 21-76, in Flow Cytometry: Instrumentation andData Analysis (Academic Press, New York, 1985).

“Substantially identical” in reference to proteins or amino acidsequences of proteins in a family of related proteins that are beingcompared means either that one protein has an amino acid sequence thatis at least fifty percent identical to the other protein or that oneprotein is an isoform or splice variant of the same gene as the otherprotein. In one aspect, substantially identical means one protein, oramino acid sequence thereof, is at least eighty percent identical to theother protein, or amino acid sequence thereof.

DETAILED DESCRIPTION OF THE INVENTION

The invention provides a method of using ErbB cell surface receptorcomplexes as biomarkers for the status of a disease or otherphysiological conditions in a biological organism, particularly a cancerstatus in a human. In one aspect, ErbB receptor complexes are measureddirectly from patient samples; that is, measurements are made withoutculturing, formation of xenografts, or the use of like techniques, thatrequire extra labor and expense and that may introduce artifacts and/ornoise into the measurement process. In a particular aspect of theinvention, measurements of one or more receptor complexes are madedirectly on tissue lysates of frozen patient samples or on sections offixed patient samples. In a preferred embodiment, one or more ErbBreceptor complexes are measured in sections of formalin-fixedparaffin-embedded (FFPE) samples.

In another aspect, the invention provides an indirect measurement ofErbB receptor phosphorylation through the measurement of complexes thatdepend on such posttranslational modifications for their formation.

In one aspect, a plurality of ErbB receptor complexes, such as receptordimers, are simultaneously measured in the same assay reaction mixture.Preferably, such complexes are measured using binding compounds havingone or more molecular tags releasably attached, such that after bindingto a protein in a complex, the molecular tags may be released andseparated from the reaction, or assay, mixture for detection and/orquantification.

In one aspect, the invention provides a method for determining a diseasestatus of a patient comprising the following steps: measuring an amountof each of one or more ErbB receptor dimers in a patient sample;comparing each such amount to its corresponding amount from a referencesample; and correlating differences in the amounts from the patientsample and the respective corresponding amounts from the referencesample to the presence or severity of a disease condition in thepatient. In a preferred embodiment, the step of measuring comprising thesteps of: (i) providing one or more binding compounds specific for aprotein of each of the one or more receptor dimers, such that eachbinding compound has one or more molecular tags each attached thereto bya cleavable linkage, and such that the one or more molecular tagsattached to different binding compounds have different separationcharacteristics so that upon separation molecular tags from differentbinding compounds form distinct peaks in a separation profile; (ii)mixing the binding compounds and the one or more complexes such thatbinding compounds specifically bind to their respective receptor dimersto form detectable complexes; (iii) cleaving the cleavable linkage ofeach binding compound forming detectable complexes, and (iv) separatingand identifying the released molecular tags to determine the presence orabsence or the amount of the one or more receptor dimers.

In another aspect, the step of measuring the amounts of one or moretypes of ErbB receptor dimer comprising the following steps: (i)providing for each of the one or more types of receptor dimer a cleavingprobe specific for a first receptor in each of the one or more receptordimers, each cleaving probe having a cleavage-inducing moiety with aneffective proximity; (ii) providing one or more binding compoundsspecific for a second receptor of each of the one or more receptordimers, such that each binding compound has one or more molecular tagseach attached thereto by a cleavable linkage, and such that the one ormore molecular tags attached to different binding compounds havedifferent separation characteristics so that upon separation moleculartags from different binding compounds form distinct peaks in aseparation profile; (iii) mixing the cleaving probes, the bindingcompounds, and the one or more types of receptor dimers such thatcleaving probes specifically bind to first receptors of the receptordimers and binding compounds specifically bind to the second receptorsof the receptor dimers and such that cleavable linkages of the bindingcompounds are within the effective proximity of cleavage-inducingmoieties of the cleaving probes so that molecular tags are released; and(iv) separating and identifying the released molecular tags to determinethe presence or absence or the amount of the one or more types ofreceptor dimers. Preferably, receptor dimers and first and secondreceptors are selected from the receptor dimers listed in Table I.

In another aspect of the invention, a biological specimen, whichcomprises a mixed cell population suspected of containing the rare cellof interest is obtained from a patient. A sample is then prepared bymixing the biological specimen with magnetic particles which are coupledto a biospecific ligand specifically reactive with an antigen on therare cell that is different from or not found on blood cells (referredto herein as a “capture antigen”), so that other sample components maybe substantially removed. The sample is subjected to a magnetic fieldwhich is effective to separate cells labeled with the magneticparticles, including the rare cells of interest, if any are present inthe specimen. The cell population so isolated is then analyzed usingmolecular tags conjugated to binding moieties specific for biomarkers todetermine the presence and/or number of rare cells. In a preferredembodiment the magnetic particles used in this method are colloidalmagnetic nanoparticles. Preferably, such rare cell populations arecirculating epithelial cells, which may be isolated from patient’s bloodusing epithelial-specific capture antigens, e.g. as disclosed in Hayeset al, International J. of Oncology, 21: 1111-1117 (2002); Soria et al,Clinical Cancer Research, 5: 971-975 (1999); Ady et al, British J.Cancer, 90: 443-448 (2004); which are incorporated by reference. Inparticular, monoclonal antibody BerEP4 (Dynal A.S., Oslo, Norway) may beused to capture human epithelial cells with magnetic particles.

In another aspect, the invention provides a method for determining acancer status of a patient comprising the following steps: (i)immunomagnetically isolating a patient sample comprising circulatingepithelial cells by contacting a sample of patient blood with one ormore antibody compositions, each antibody composition being specific fora capture antigen and being attached to a magnetic particle; (ii)measuring an amount of each of one or more ErbB receptor complexes inthe patient sample; comparing each such amount to its correspondingamount from a reference sample; and correlating differences in theamounts from the patient sample and the respective corresponding amountsfrom the reference sample to the presence or severity of a cancercondition in the patient. In a preferred embodiment, the step ofmeasuring comprises the steps of: (i) providing one or more bindingcompounds specific for a protein of each of the one or more ErbBreceptor complexes, such that each binding compound has one or moremolecular tags each attached thereto by a cleavable linkage, and suchthat the one or more molecular tags attached to different bindingcompounds have different separation characteristics so that uponseparation molecular tags from different binding compounds form distinctpeaks in a separation profile; (ii) mixing the binding compounds and theone or more ErbB receptor complexes such that binding compoundsspecifically bind to their respective proteins of the one or more ErbBreceptor complexes to form detectable complexes; (iii) cleaving thecleavable linkage of each binding compound forming detectable complexes,and (iv) separating and identifying the released molecular tags todetermine the presence or absence or the amount of the one or more ErbBreceptor complexes.

In another aspect, the step of measuring the amounts of one or more ErbBreceptor complexes comprising the following steps: (i) providing foreach of the one or more ErbB receptor complexes a cleaving probespecific for a first protein in each of the one or more ErbB receptorcomplexes, each cleaving probe having a cleavage-inducing moiety with aneffective proximity; (ii) providing one or more binding compoundsspecific for a second protein of each of the one or more ErbB receptorcomplexes, such that each binding compound has one or more moleculartags each attached thereto by a cleavable linkage, and such that the oneor more molecular tags attached to different binding compounds havedifferent separation characteristics so that upon separation moleculartags from different binding compounds form distinct peaks in aseparation profile; (iii) mixing the cleaving probes, the bindingcompounds, and the one or more complexes such that cleaving probesspecifically bind to first proteins of the ErbB receptor complexes andbinding compounds specifically bind to the second proteins of the ErbBreceptor complexes and such that cleavable linkages of the bindingcompounds are within the effective proximity of cleavage-inducingmoieties of the cleaving probes so that molecular tags are released; and(iv) separating and identifying the released molecular tags to determinethe presence or absence or the amount of the one or more ErbB receptorcomplexes.

Exemplary Receptor Dimer Biomarkers and Dimer-Acting Drugs

Biomarkers of the invention include dimers and oligomers of thefollowing receptors. Table I. Exemplary Receptor Complexes of CellSurface Membranes Dimer Dimer Her1-Her1 IGF-1R-Her1 heterodimerHer1-Her2 IGF-1R-Her3 heterodimer Her1-Her3 Her1-PDGFR heterodimersHer1-Her4 Her3-PDGFR heterodimers Her2-Her2 Her2-PI3K Her2-Her3 Her1-SHCHer2-Her4 Her3-SHC Her3-Her4 Her2-SHC Her4-Her4 Her3-PI3K Her2-PDGFRheterodimers Her1-PI3K IGF-1R-Her2 heterodimer

The mechanisms of action of many drugs that are in use or are underdevelopment require the inhibition of one or more functions of ErbBreceptor dimers, such as the association of component receptors into adimer structure, or a function, such as an enzymatic activity, e.g.kinase activity, or autophosphorylation, that depends on dimerization.Such drugs are referred to herein as “dimer-acting” drugs, or “ErbBdimer-acting” drugs. The number, type, formation, and/or dissociation ofreceptor dimers in the cells of a patient being treated, or whosetreatment is contemplated, have a bearing on the effectiveness orsuitability of using a particular ErbB dimer-acting drug. The followingErbB receptor dimers are biomarkers related to the indicated drugs. Inone aspect, the invention provides biomarkers for monitoring the effecton disease status of an ErbB dimer-acting drug. Table II. DrugsAssociated with Dimers of Cell Surface Membranes Dimer Drug(s)Her1-Her1, Her1-Her2, Her1-Her3, Her1-Her4, Her1-IGF-1R, Her2-IGF-1RCetuximab (Erbitux), Trastuzumab (Herceptin), h-R3 (TheraCIM), ABX-EGF,MDX-447, ZD-1839 (Iressa), OSI-774 (Tarceva), PKI 166, GW572016,CI-1033, EKB-569, EMD 72000 Her2-Her1, Her2-Her3, Her2-Her2, Her2-Her44D4 Mab, Trastuzumab (Herceptin), 2C4, GW572016

The following references describe the dimer-acting drugs listed in TableII: Traxler, Expert Opin. Ther. Targets, 7: 215-234 (2002); Baselga,editor, Oncology Biotherapeutics, 2: 1-36 (2002); Nam et al, CurrentDrug Targets, 4: 159-179 (2003); Seymour, Current Drug Targets, 2:117-133 (2001); and the like. Table III. PI3K-Associated ReceptorComplexes Dimer Dimer Her1-Her1 IGF-1R-Her1 heterodimer Her1-Her2Her4-Her4 Her1-Her3 Her3-Her4 Her1-Her4 Her2-Her4 Her2-Her2 Her2-Her3IGF-1R-Her2 heterodimer IGF-1R-Her3 heterodimer Her3-PDGFR heterodimersHer1-PDGFR heterodimers Her2-PDGFR heterodimers Her2-XX-PI3K* * “XX”refers to any receptor Her2 is capable of forming a dimer with.

Preparation of Samples

Samples containing molecular complexes may come from a wide variety ofsources for use with the present invention to relate receptor complexespopulations to disease status or health status, including cell cultures,animal or plant tissues, patient biopsies, or the like. Preferably,samples are human patient samples. Samples are prepared for assays ofthe invention using conventional techniques, which may depend on thesource from which a sample is taken.

A. Solid Tissue Samples. For biopsies and medical specimens, guidance isprovided in the following references: Bancroft JD & Stevens A, eds.Theory and Practice of Histological Techniques (Churchill Livingstone,Edinburgh, 1977); Pearse, Histochemistry. Theory and applied. 4^(th) ed.(Churchill Livingstone, Edinburgh, 1980).

In the area of cancerous disease status, examples of patient tissuesamples that may be used include, but are not limited to, breast,prostate, ovary, colon, lung, endometrium, stomach, salivary gland orpancreas. The tissue sample can be obtained by a variety of proceduresincluding, but not limited to surgical excision, aspiration or biopsy.The tissue may be fresh or frozen. In one embodiment, assays of theinvention are carried out on tissue samples that have been fixed andembedded in paraffin or the like; therefore, in such embodiments a stepof deparaffination is carried out. A tissue sample may be fixed (i.e.preserved) by conventional methodology [See e.g., "Manual ofHistological Staining Method of the Armed Forces Institute ofPathology," 3^(rd) edition (1960) Lee G. Luna, HT (ASCP) Editor, TheBlakston Division McGraw-Hill Book Company, New York; The Armed ForcesInstitute of Pathology Advanced Laboratory Methods in Histology andPathology (1994) Ulreka V. Mikel, Editor, Armed Forces Institute ofPathology, American Registry of Pathology, Washington, D.C One of skillin the art will appreciate that the choice of a fixative is determinedby the purpose for which the tissue is to be histologically stained orotherwise analyzed. One of skill in the art will also appreciate thatthe length of fixation depends upon the size of the tissue sample andthe fixative used. By way of example, neutral buffered formalin, Bouin'sor paraformaldehyde, may be used to fix a tissue sample.

Generally, a tissue sample is first fixed and is then dehydrated throughan ascending series of alcohols, infiltrated and embedded with paraffinor other sectioning media so that the tissue sample may be sectioned.Alternatively, one may section the tissue and fix the sections obtained.By way of example, the tissue sample may be embedded and processed inparaffin by conventional methodology (See e.g., "Manual of HistologicalStaining Method of the Armed Forces Institute of Pathology", supra).Examples of paraffin that may be used include, but are not limited to,Paraplast, Broloid, and Tissuemay. Once the tissue sample is embedded,the sample may be sectioned by a microtome or the like (See e.g.,"Manual of Histological Staining Method of the Armed Forces Institute ofPathology", supra). By way of example for this procedure, sections mayhave a thickness in a range from about three microns to about twelvemicrons, and preferably, a thickness in a range of from about 5 micronsto about 10 microns. In one aspect, a section may have an area of fromabout 10 mm² to about 1 cm². Once cut, the sections may be attached toslides by several standard methods. Examples of slide adhesives include,but are not limited to, silane, gelatin, poly-L-lysine and the like. Byway of example, the paraffin embedded sections may be attached topositively charged slides and/or slides coated with poly-L-lysine.

If paraffin has been used as the embedding material, the tissue sectionsare generally deparaffinized and rehydrated to water. The tissuesections may be deparaffinized by several conventional standardmethodologies. For example, xylenes and a gradually descending series ofalcohols may be used (See e.g., "Manual of Histological Staining Methodof the Armed Forces Institute of Pathology", supra). Alternatively,commercially available deparaffinizing non-organic agents such asHemo-De (CMS, Houston, Tex.) may be used.

For mammalian tissue culture cells, fresh tissues, or like sources,samples may be prepared by conventional cell lysis techniques (e.g. 0.14M NaCl, 1.5 mM MgCl₂, 10 mM Tris-Cl (pH 8.6), 0.5% Nonidet P-40, andprotease and/or phosphatase inhibitors as required). For fresh mammaliantissues, sample preparation may also include a tissue disaggregationstep, e.g. crushing, mincing, grinding, sonication, or the like.

B. Magnetic Isolation of Cells. In some applications, such as measuringdimers on rare metastatic cells from a patient’s blood, an enrichmentstep may be carried out prior to conducting an assay for surfacereceptor dimer populations. Immunomagnetic isolation or enrichment maybe carried out using a variety of techniques and materials known in theart, as disclosed in the following representative references that areincorporated by reference: Terstappen et al, U.S. patent 6,365,362;Terstappen et al, U.S. patent 5,646,001; Rohr et al, U.S. patent5,998,224; Kausch et al, U.S. patent 5,665,582; Kresse et al, U.S.patent 6,048,515; Kausch et al, U.S. patent 5,508,164; Miltenyi et al,U.S. patent 5,691,208; Molday, U.S. patent 4,452,773; Kronick, U.S.patent 4,375,407; Radbruch et al, chapter 23, in Methods in CellBiology, Vol, 42 (Academic Press, New York, 1994); Uhlen et al, Advancesin Biomagnetic Separation (Eaton Publishing, Natick, 1994); Safarik etal, J. Chromatography B, 722: 33-53 (1999); Miltenyi et al, Cytometry,11: 231-238 (1990); Nakamura et al, Biotechnol. Prog., 17: 1145-1155(2001); Moreno et al, Urology, 58: 386-392 (2001); Racila et al, Proc.Natl. Acad. Sci., 95: 4589-4594 (1998); Zigeuner et al, J. Urology, 169:701-705 (2003); Ghossein et al, Seminars in Surgical Oncology, 20:304-311 (2001).

The preferred magnetic particles for use in carrying out this inventionare particles that behave as colloids. Such particles are characterizedby their sub-micron particle size, which is generally less than about200 nanometers (nm) (0.20 microns), and their stability to gravitationalseparation from solution for extended periods of time. In addition tothe many other advantages, this size range makes them essentiallyinvisible to analytical techniques commonly applied to cell analysis.Particles within the range of 90-150 nm and having between 70-90%magnetic mass are contemplated for use in the present invention.Suitable magnetic particles are composed of a crystalline core ofsuperparamagnetic material surrounded by molecules which are bonded,e.g., physically absorbed or covalently attached, to the magnetic coreand which confer stabilizing colloidal properties. The coating materialshould preferably be applied in an amount effective to prevent nonspecific interactions between biological macromolecules found in thesample and the magnetic cores. Such biological macromolecules mayinclude sialic acid residues on the surface of non-target cells,lectins, glyproteins and other membrane components. In addition, thematerial should contain as much magnetic mass/nanoparticle as possible.The size of the magnetic crystals comprising the core is sufficientlysmall that they do not contain a complete magnetic domain. The size ofthe nanoparticles is sufficiently small such that their Brownian energyexceeds their magnetic moment. As a consequence, North Pole, South Polealignment and subsequent mutual attraction/repulsion of these colloidalmagnetic particles does not appear to occur even in moderately strongmagnetic fields, contributing to their solution stability. Finally, themagnetic particles should be separable in high magnetic gradientexternal field separators. That characteristic facilitates samplehandling and provides economic advantages over the more complicatedinternal gradient columns loaded with ferromagnetic beads or steel wool.Magnetic particles having the above-described properties can be preparedby modification of base materials described in U.S. Pat. Nos. 4,795,698,5,597,531 and 5,698,271, which patents are incorporated by reference.

Assays Using Releasable Molecular Tags

Many advantages are provided by measuring dimer populations usingreleasable molecular tags, including (1) separation of releasedmolecular tags from an assay mixture provides greatly reduced backgroundand a significant gain in sensitivity; and (2) the use of molecular tagsthat are specially designed for ease of separation and detectionprovides a convenient multiplexing capability so that multiple receptorcomplex components may be readily measured simultaneously in the sameassay. Assays employing such tags can have a variety of forms and aredisclosed in the following references: Singh et al, U.S. patent6,627,400; U.S. patent publications Singh et al, 2002/0013126; and2003/0170915, and Williams et al, 2002/0146726; and Chan-Hui et al,International patent publication WO 2004/011900, all of which areincorporated herein by reference.. For example, a wide variety ofseparation techniques may be employed that can distinguish moleculesbased on one or more physical, chemical, or optical differences amongmolecules being separated including but not limited to electrophoreticmobility, molecular weight, shape, solubility, pKa, hydrophobicity,charge, charge/mass ratio, polarity, or the like. In one aspect,molecular tags in a plurality or set differ in electrophoretic mobilityand optical detection characteristics and are separated byelectrophoresis. In another aspect, molecular tags in a plurality or setmay differ in molecular weight, shape, solubility, pKa, hydrophobicity,charge, polarity, and are separated by normal phase or reverse phaseHPLC, ion exchange HPLC, capillary electrochromatography, massspectroscopy, gas phase chromatography, or like technique.

Sets of molecular tags are provided that are separated into distinctbands or peaks by a separation technique after they are released frombinding compounds. Identification and quantification of such peaksprovides a measure or profile of the kinds and amounts of receptordimers. Molecular tags within a set may be chemically diverse; however,for convenience, sets of molecular tags are usually chemically related.For example, they may all be peptides, or they may consist of differentcombinations of the same basic building blocks or monomers, or they maybe synthesized using the same basic scaffold with different substituentgroups for imparting different separation characteristics, as describedmore fully below. The number of molecular tags in a plurality may varydepending on several factors including the mode of separation employed,the labels used on the molecular tags for detection, the sensitivity ofthe binding moieties, the efficiency with which the cleavable linkagesare cleaved, and the like. In one aspect, the number of molecular tagsin a plurality for measuring populations of receptor dimers is in therange of from 2 to 10. In other aspects, the size of the plurality maybe in the range of from 2 to 8, 2 to 6, 2 to 4, or 2 to 3.

Receptor dimers may be detected in assays having homogeneous formats ora non-homogeneous, i.e. heterogeneous, formats. In a homogeneous format,no step is required to separate binding compounds specifically bound totarget complexes from unbound binding compounds. In a preferredembodiment, homogeneous formats employ reagent pairs comprising (i) oneor more binding compounds with releasable molecular tags and (ii) atleast one cleaving probe that is capable of generating an active speciesthat reacts with and releases molecular tags within an effectiveproximity of the cleaving probe.

Receptor dimers may also be detected by assays employing a heterogeneousformat. Heterogeneous techniques normally involve a separation step,where intracellular complexes having binding compounds specificallybound are separated from unbound binding compounds, and optionally,other sample components, such as proteins, membrane fragments, and thelike. Separation can be achieved in a variety of ways, such as employinga reagent bound to a solid support that distinguishes betweencomplex-bound and unbound binding compounds. The solid support may be avessel wall, e.g., microtiter well plate well, capillary, plate, slide,beads, including magnetic beads, liposomes, or the like. The primarycharacteristics of the solid support are that it (1) permits segregationof the bound and unbound binding compounds and (2) does not interferewith the formation of the binding complex, or the other operations inthe determination of receptor dimers. Usually, in fixed samples, unboundbinding compounds are removed simply by washing.

With detection using molecular tags in a heterogeneous format, afterwashing, a sample may be combined with a solvent into which themolecular tags are to be released. Depending on the nature of thecleavable bond and the method of cleavage, the solvent may include anyadditional reagents for the cleavage. Where reagents for cleavage arenot required, the solvent conveniently may be a separation buffer, e.g.an electrophoretic separation medium. For example, where the cleavablelinkage is photolabile or cleavable via an active species generated by aphotosensitizer, the medium may be irradiated with light of appropriatewavelength to release the molecular tags into the buffer.

In either format, if the assay reaction conditions interfere with theseparation technique employed, it may be necessary to remove, orexchange, the assay reaction buffer prior to cleavage and separation ofthe molecular tags. For example, in some embodiments, assay conditionsinclude salt concentrations (e.g. required for specific binding) thatdegrade separation performance when molecular tags are separated on thebasis of electrophoretic mobility. In such embodiments, an assay bufferis replaced by a separation buffer, or medium, prior to release andseparation of the molecular tags.

Assays employing releasable molecular tags and cleaving probes can bemade in many different formats and configuations depending on thecomplexes that are detected or measured. Based on the presentdisclosure, it is a design choice for one of ordinary skill in the artto select the numbers and specificities of particular binding compoundsand cleaving probes.

In one aspect of the invention, the use of releasable molecular tags tomeasure dimers of cell surface membranes is shown diagrammatically inFigs. 1A and 1B. Binding compounds (100) having molecular tags “mT₁” and“mT₂” and cleaving probe (102) having photosensitizer “PS” are combinedwith biological cells (104). Binding compounds having molecular tag“mT₁” are specific for cell surface receptors R₁ (106) and bindingcompounds having molecular tag “mT₂” are specific for cell surfacereceptors R₂ (108). Cell surface receptors R₁ and R₂ are present asmonomers, e.g. (106) and (108), and as dimers (110) in cell surfacemembrane (112). After these assay components are incubated in a suitablebinding buffer to permit the formation (114) of stable complexes betweenbinding compounds and their respective receptor targets and between thecleaving probe and its receptor target. As illustrated, preferablybinding compounds and cleaving probes each comprise an antibody bindingcomposition, which permits the molecular tags and cleavage-inducingmoiety to be specifically targeted to membrane components. In oneaspect, such antibody binding compositions are monoclonal antibodies. Insuch embodiments, binding buffers may comprise buffers used inconventional ELISA techniques, or the like. After binding compounds andcleaving probes for stable complexes (116), the assay mixture isilluminated (118) to induce photosensitizers (120) to generate singletoxygen. Singlet oxygen rapidly reacts with components of the assaymixture so that its effective proximity (122) for cleaving cleavablelinkages of molecular tags is spatially limited so that only moleculartags that happen to be within the effective proximity are released(124). As illustrated, the only molecular tags released are those onbinding compounds that form stable complexes with R₁-R₂ dimers and acleaving probe. Released molecular tags (126) are removed from the assaymixture and separated (128) in accordance with a separationcharacteristic so that a distinct peak (130) is formed in a separationprofile (132). In accordance with the invention, such removal andseparation may be the same step. Optionally, prior to illumination thebinding buffer may be removed and replaced with a buffer more suitablefor separation, i.e. a separation buffer. For example, binding bufferstypically have salt concentrations that may degrade the performance ofsome separation techniques, such as capillary electrophoresis, forseparating molecular tags into distinct peaks. In one embodiment, suchexchange of buffers may be accomplished by membrane filtration.

An embodiment that illustrates ratiometric measurement of heterodimersis illustrated in Fig. 1C, in which an additional binding compound isemployed to give a measure of the total amount of protein (1104) in asample. Reagents (1122) of the invention comprise (i) cleaving probes(1108), first binding compound (1106), and second binding compound(1107), wherein first binding compound (1106) is specific for protein(1102) and second binding compound (1107) is specific for protein (1104)at a different antigenic determinant than that cleaving probe (1108) isspecific for. After binding of the reagents, cleaving probe (1108) isactivated to produce active species that cleave the cleavable linkagesof the molecular tags within the effective proximity of thephotosensitizer. In this embodiment, molecular tags are released frommonomers of protein (1104) that have both reagents (1107) and (1108)attached and from heterodimers that have reagent (1108) attached andeither or both of reagents (1106) and (1107) attached. Releasedmolecular tags (1123) are separated, and peaks (1118 and 1124) in aseparation profile (1126) are correlated to the amounts of the releasedmolecular tags. In this embodiment, relative peak heights, or areas, mayreflect (i) the differences in affinity of the first and second bindingcompounds for their respective antigenic determinants, and/or (ii) thepresence or absense of the antigenic determinant that the bindingcompound is specific for. The later situation is important whenever abinding compound is used to monitor the post-translational state of aprotein, e.g. phosphorylation state.

Homodimers may be measured as illustrated in Fig. 1D. As above, an assaymay comprise three reagents (1128): cleaving probes (1134), firstbinding compound (1130), and second binding compound (1132). Firstbinding compound (1130) and cleaving probe (1134) are constructed to bespecific for the same antigenic determinant (1135) on protein (1138)that exists (1140) in a sample as either a homodimer (1136) or a monomer(1138). After reagents (1128) are combined with a sample underconditions that promote the formation of stable complexes between thereagents and their respective targets, multiple complexes (1142 through1150) form in the assay mixture. Because cleaving probe (1134) andbinding compound (1130) are specific for the same antigenic determinant(1135), four different combinations (1144 through 1150) of reagents mayform complexes with homodimers. Of the complexes in the assay mixture,only those (1143) with both a cleaving probe (1134) and at least onebinding compound will contribute released molecular tags (1151) forseparation and detection (1154). In this embodiment, the size of peak(1153) is proportional to the amount of homodimer in the assay mixture,while the size of peak (1152) is proportional to the total amount ofprotein (1138) in the assay mixture, both in monomeric form (1142) or inhomodimeric form (1146 and 1148). Fig. 1E illustrates the analogousmeasurements for cell surface receptors that form heterodimers in cellsurface membrane (1161). One skilled in the art would understand thatdimers may be measured in either lysates of cells or tissues, or infixed samples whose membranes have been permeabilized or removed by thefixing process. In such cases, binding compounds may be specific foreither extracellular or intracellular domains of cell surface membranereceptors.

As illustrated in Figs. 1E and 1F, releasable molecular tags may also beused for the simultaneous detection or measurement of multiple dimersand intracellular complexes in a cellular sample. Cells (160), which maybe from a sample from in vitro cultures or from a specimen of patienttissue, are lysed (172) to render accessable molecular complexesassociated with the cell membrane, and/or post-translationalmodification sites, such as phosphorylation sites, within thecytoplasmic domains of the membrane molecules. After lysing, theresulting lysate (174) is combined with assay reagents (176) thatinclude multiple cleaving probes (175) and multiple binding compounds(177). Assay conditions are selected (178) that allow reagents (176) tospecifically bind to their respective targets, so that upon activationcleavable linkages within the effective proximity (180) of thecleavage-inducing moieties are cleaved and molecular tags are released(182). As above, after cleavage, the released molecular tags areseparated (184) and identified in a separation profile (186), such as anelectropherogram, and based on the number and quantities of moleculartags measured, a profile is obtained of the selected molecular complexesin the cells of the sample.

Figs. 1G and 1H illustrate an embodiment of the invention for measuringreceptor complexes in fixed or frozen tissue samples. Fixed tissuesample (1000), e.g. a formalin-fixed paraffin-embedded sample, is slicedto provide a section (1004) using a microtome, or like instrument, whichafter placing on surface (1006), which may be a microscope slide, it isde-waxed and re-hydrated for application of assay reagents. Enlargement(1007) shows portion (1008) of section (1004) on portion (1014) ofmicroscope slide (1006). Receptor dimer molecules (1018) are illustratedas embedded in the remnants of membrane structure (1016) of the fixedsample. In accordance with this aspect of the invention, cleaving probeand binding compounds are incubated with the fixed sample so that theybind to their target molecules. For example, cleaving probes(1012)(illustrated in the figure as an antibody having a photosensitizer(“PS”) attached) and first binding compound (1010)(illustrated as anantibody having molecular tag “mT₁” attached) specifically bind toreceptor (1011) common to all of the dimers shown, second bindingcompound (1017)(with “mT₂”) specifically binds to receptor (1015), andthird binding compound (1019)(with “mT₃”) specifically binds to receptor(1013). After washing to remove binding compounds and cleaving probethat are not specifically bound to their respective target molecules,buffer (1024) (referred to as “illumination buffer” in the figure) isadded. For convenience, buffer (1024) may be contained on section(1004), or a portion thereof, by creating a hydrophobic barrier on slide(1006), e.g. with a wax pen. After illumination of photosensitizers andrelease of molecular tags (1026), buffer (1024) now containing releasemolecular tags (1025) is transferred to a separation device, such as acapillary electrophoresis instrument, for separation (1028) andidentification of the released molecular tags in, for example,electropherogram (1030).

Measurements made directly on tissue samples, particularly asillustrated in Figs. 1G and 1H, may be normalized by includingmeasurements on cellular or tissue targets that are representative ofthe total cell number in the sample and/or the numbers of particularsubtypes of cells in the sample. Such tissue targets are referred toherein as “tissue indicators.” The additional measurement may bepreferred, or even necessary, because of the cellular and tissueheterogeneity in patient samples, particularly tumor samples, which maycomprise substantial fractions of normal cells. For example, in Fig. 1H,values for the total amount of receptor (1011) may be given as a ratioof the following two measurements: area of peak (1032) of molecular tag(“mT₁”) and the area of a peak corresponding to a molecular tagcorrelated with a cellular or tissue component common to all the cellsin the sample, e.g. tubulin, or the like. In some cases, where all thecells in the sample are epithelial cells, cytokeratin may be used.Accordingly, detection methods based on releasable molecular tags mayinclude an additional step of providing a binding compound (with adistinct molecular tag) specific for a normalization protein, such astubulin.

Figures 2A-2E illustrate another embodiment of the invention forprofiling dimerization among a plurality of receptor types. Figure 2Aoutlines the basic steps of such an assay. Cell membranes (200) that areto be tested for dimers of cell surface receptors are combined with setsof binding compounds (202) and (204) and cleaving probe (206). Membranefractions (200) contain three different types of monomer receptormolecules (“1,” “2,” and “3”) in its cell membrane which associate toform three different heterodimers: 1-2, 1-3, and 2-3. Three antibodyreagents (202) and (204) are combined with membrane fraction (200), eachof the antibody reagents having binding specificity for one of the threereceptor molecules, where antibody (206) is specific for receptormolecule 1, antibody (204) is specific for receptor molecule 2, andantibody (202) is specific for receptor molecule 3. The antibody for thefirst receptor molecule is covalently coupled to a photosensitizermolecule, labeled PS. The antibodies for the second and third receptormolecules are linked to two different tags, labeled T₂ and T₃,respectively, through a linkage that is cleavable by an active speciesgenerated by the photosensitizer moiety.

After mixing, the antibodies are allowed to bind (208) to molecules onthe surface of the membranes. The photosensitizer is activated (210),cleaving the linkage between tags and antibodies that are within anactionable distance from a sensitizer molecule, thereby releasing tagsinto the assay medium. Material from the reaction is then separated(212), e.g., by capillary electrophoresis, as illustrated. As shown atthe bottom of Figure 2A, the tags T₂ and T₃ are released, and separationby electrophoresis will reveal two bands corresponding to these tags.Because the tags are designed to have a known electrophoretic mobility,each of the bands can be uniquely assigned to one of the tags used inthe assay.

As shown in Fig. 2A, only two of the three different heterodimers thatare present in the cell membrane will bind both aphotosensitizer-containing antibody and a tag-containing antibody, andthus only these two species should give rise to released tags. However,multiple experiments are required to measure the relative amounts of thedifferent dimers. Fig. 2B provides a table listing five different assaycombinations. In Fig. 2C are the illustrative results for each assaycomposition. Assay I represents the results from the complete assay, asdescribed in Figure 2A. In Assay II, the antibody specific for receptormolecule 1, which is linked to the photosensitizer, is omitted. Thisassay yields no signal, indicating that the T₂ and T₃ signals obtainedin Assay I require the photosensitizer reagent. Similarly, Assay V showsthat the tag signals require the presence of the membranes. Assays IIIand IV show that each tagged reagent does not require the presence ofthe other to be cleaved. These results, when considered together, allowone to draw conclusions regarding the presence and composition ofreceptor heterodimers present in the membrane, as given in Figure 2C,i.e., that both the 1-2 and the 1-3 heterodimer are present.Furthermore, the relative signal intensities from each tag allow one toestimate the relative abundance of each of the heterodimers.

A conclusion regarding existence of the 2-3 heterodimer cannot be madewith the combination of reagents used in this assay, however. No signalrepresenting this complex will be obtained, whether or not the complexis present, because it will not have a photosensitizer reagent bound toit. In order to draw conclusions regarding every possible dimericcombination of the three monomers, either a fourth reagent must be usedthat can be localized to every possible oligomer comprising monomers 1,2, and/or 3, or the three binding agents used in this experiment must becoupled in different combinations to tags and sensitizer molecules. Thelater strategy is illustrated in Figures 2D and 2E. Three possiblecombinations of photosensitizer and tag distribution among the threeantibody reagents are listed in the table on the left of Figure 2D. Thefirst combination comprises a photosensitizer coupled to the antibodyspecific for monomer number 1, and is the same combination used in theillustration of Figure 2A-2C, and has the same dimer population as inFigure 2C. The second combination comprises a photosensitizer coupled tothe antibody specific for monomer number 2, and the population profileyields the same number for heterodimer 1-2, plus a value for heterodimer2-3. The third combination comprises a photosensitizer coupled to theantibody specific for monomer number 3, and the population profileyields the same number for heterodimer 1-3 and 2-3 as obtained from thefirst two combinations. These results can be combined to yield theoverall heterodimer population profile given in Figure 2E.

A preferred embodiment for measuring relative amounts of receptor dimerscontaining a common component receptor is illustrated in Fig. 2F. Inthis assay design, two different receptor dimers (“1-2” (240) and “2-3”(250)) each having a common component, “2,” may be measuredratiometrically with respect to the common component. An assay design isshown for measuring receptor heterodimer (240) comprising receptor “1”(222) and receptor “2” (220) and receptor heterodimer (250) comprisingreceptor “2” (220) and receptor “3”(224). A key feature of thisembodiment is that cleaving probe (227) be made specific for the commonreceptor of the pair of heterodimers. Binding compound (228) specificfor receptor “2” provides a signal (234) related to the total amount ofreceptor “2” in the assay, whereas binding compound (226) specific forreceptor “1” and binding compound (230) specific for receptor “3”provide signals (232 and 236, respectively) related only to the amountof receptor “1” and receptor “3” present as heterodimers with receptor“2,” respectively. The design of Fig. 2F may be generalized to more thantwo receptor complexes that contain a common component by simply addingbinding compounds specific for the components of the additionalcomplexes.

A. Binding Compounds

As mentioned above, mixtures containing pluralities of different bindingcompounds may be provided, wherein each different binding compound hasone or more molecular tags attached through cleavable linkages. Thenature of the binding compound, cleavable linkage and molecular tag mayvary widely. A binding compound may comprise an antibody bindingcomposition, an antibody, a peptide, a peptide or non-peptide ligand fora cell surface receptor, a protein, an oligonucleotide, anoligonucleotide analog, such as a peptide nucleic acid, a lectin, or anyother molecular entity that is capable of specifically binding to atarget protein or molecule or stable complex formation with an analyteof interest, such as a complex of proteins. In one aspect, a bindingcompound, which can be represented by the formula below, comprises oneor more molecular tags attached to a binding moiety.

B-(L-E)_(k)

wherein B is binding moiety; L is a cleavable linkage; and E is amolecular tag. In homogeneous assays, cleavable linkage, L, may be anoxidation-labile linkage, and more preferably, it is a linkage that maybe cleaved by singlet oxygen. The moiety “-(L-E)_(k)” indicates that asingle binding compound may have multiple molecular tags attached viacleavable linkages. In one aspect, k is an integer greater than or equalto one, but in other embodiments, k may be greater than several hundred,e.g. 100 to 500, or k is greater than several hundred to as many asseveral thousand, e.g. 500 to 5000. Usually each of the plurality ofdifferent types of binding compound has a different molecular tag, E.Cleavable linkages, e.g. oxidation-labile linkages, and molecular tags,E, are attached to B by way of conventional chemistries.

Preferably, B is an antibody binding composition that specifically bindsto a target, such as a predetermined antigenic determinant of a targetprotein, such as a cell surface receptor. Such compositions are readilyformed from a wide variety of commercially available antibodies, eithermonoclonal and polyclonal, specific for proteins of interest. Inparticular, antibodies specific for epidermal growth factor receptorsare disclosed in the following patents, which are incorporated byreferences: 5,677,171; 5,772,997; 5,968,511; 5,480,968; 5,811,098. U.S.patent 6,488,390, incorporated herein by reference, discloses antibodiesspecific for a G-protein coupled receptor, CCR4. U.S. patent 5,599,681,incorporated herein by reference, discloses antibodies specific forphosphorylation sites of proteins. Commercial vendors, such as CellSignaling Technology (Beverly, MA), Biosource International (Camarillo,CA), and Upstate (Charlottesville, VA), also provide monoclonal andpolyclonal antibodies specific for many receptors.

Cleavable linkage, L, can be virtually any chemical linking group thatmay be cleaved under conditions that do not degrade the structure oraffect detection characteristics of the released molecular tag, E.Whenever a cleaving probe is used in a homogeneous assay format,cleavable linkage, L, is cleaved by a cleavage agent generated by thecleaving probe that acts over a short distance so that only cleavablelinkages in the immediate proximity of the cleaving probe are cleaved.Typically, such an agent must be activated by making a physical orchemical change to the reaction mixture so that the agent produces ashort lived active species that diffuses to a cleavable linkage toeffect cleavage. In a homogeneous format, the cleavage agent ispreferably attached to a binding moiety, such as an antibody, thattargets prior to activation the cleavage agent to a particular site inthe proximity of a binding compound with releasable molecular tags. Insuch embodiments, a cleavage agent is referred to herein as a“cleavage-inducing moiety,” which is discussed more fully below.

In a non-homogeneous format, because specifically bound bindingcompounds are separated from unbound binding compounds, a widerselection of cleavable linkages and cleavage agents are available foruse. Cleavable linkages may not only include linkages that are labile toreaction with a locally acting reactive species, such as hydrogenperoxide, singlet oxygen, or the like, but also linkages that are labileto agents that operate throughout a reaction mixture, such asbase-labile linkages, photocleavable linkages, linkages cleavable byreduction, linkages cleaved by oxidation, acid-labile linkages, peptidelinkages cleavable by specific proteases, and the like. Referencesdescribing many such linkages include Greene and Wuts, Protective Groupsin Organic Synthesis, Second Edition (John Wiley & Sons, New York,1991); Hermanson, Bioconjugate Techniques (Academic Press, New York,1996); and Still et al, U.S. patent 5,565,324.

In one aspect, commercially available cleavable reagent systems may beemployed with the invention. For example, a disulfide linkage may beintroduced between an antibody binding composition and a molecular tagusing a heterofunctional agent such as N-succinimidyl3-(2-pyridyldithio)propionate (SPDP),succinimidyloxycarbonyl-alpha-methyl-alpha-(2-pyridyldithio)toluene(SMPT), or the like, available from vendors such as Pierce ChemicalCompany (Rockford, IL). Disulfide bonds introduced by such linkages canbe broken by treatment with a reducing agent, such as dithiothreitol(DTT), dithioerythritol (DTE), 2-mercaptoethanol, sodium borohydride, orthe like. Typical concentrations of reducing agents to effect cleavageof disulfide bonds are in the range of from 10 to 100 mM. An oxidativelylabile linkage may be introduced between an antibody binding compositionand a molecular tag using the homobifunctional NHS ester cross-linkingreagent, disuccinimidyl tartarate (DST)(available from Pierce) thatcontains central cis-diols that are susceptible to cleavage with sodiumperiodate (e.g., 15 mM periodate at physiological pH for 4 hours).Linkages that contain esterified spacer components may be cleaved withstrong nucleophilic agents, such as hydroxylamine, e.g. 0.1 Nhydroxylamine, pH 8.5, for 3-6 hours at 37 degrees C. Such spacers canbe introduced by a homobifunctional cross-linking agent such as ethyleneglycol bis(succinimidylsuccinate)(EGS) available from Pierce (Rockford,IL). A base labile linkage can be introduced with a sulfone group.Homobifunctional cross-linking agents that can be used to introducesulfone groups in a cleavable linkage includebis[2-(succinimidyloxycarbonyloxy)ethyl]sulfone (BSOCOES), and4,4-difluoro-3,3-dinitrophenylsulfone (DFDNPS). Exemplary basicconditions for cleavage include 0.1 M sodium phosphate, adjusted to pH11.6 by addition of Tris base, containing 6 M urea, 0.1% SDS, and 2 mMDTT, with incubation at 37 degrees C for 2 hours. Photocleavablelinkages include those disclosed in Rothschild et al, U.S. patent5,986,076.

When L is oxidation labile, L may be a thioether or its selenium analog;or an olefin, which contains carbon-carbon double bonds, whereincleavage of a double bond to an oxo group, releases the molecular tag,E. Illustrative oxidation labile linkages are disclosed in Singh et al,U.S. patent 6,627,400; and U.S. patent publications Singh et al,2002/0013126; and 2003/0170915, and in Willner et al, U.S. patent5,622,929, all of which are incorporated herein by reference.

Molecular tag, E, in the present invention may comprise an electrophorictag as described in the following references when separation ofpluralities of molecular tags are carried out by gas chromatography ormass spectrometry: Zhang et al, Bioconjugate Chem., 13: 1002-1012(2002); Giese, Anal. Chem., 2: 165-168 (1983); and U.S. patents4,650,750; 5,360,819; 5,516,931; 5,602,273; and the like.

Molecular tag, E, is preferably a water-soluble organic compound that isstable with respect to the active species, especially singlet oxygen,and that includes a detection or reporter group. Otherwise, E may varywidely in size and structure. In one aspect, E has a molecular weight inthe range of from about 50 to about 2500 daltons, more preferably, fromabout 50 to about 1500 daltons. Preferred structures of E are describedmore fully below. E may comprise a detection group for generating anelectrochemical, fluorescent, or chromogenic signal. In embodimentsemploying detection by mass, E may not have a separate moiety fordetection purposes. Preferably, the detection group generates afluorescent signal.

Molecular tags within a plurality are selected so that each has a uniqueseparation characteristic and/or a unique optical property with respectto the other members of the same plurality. In one aspect, thechromatographic or electrophoretic separation characteristic isretention time under set of standard separation conditions conventionalin the art, e.g. voltage, column pressure, column type, mobile phase,electrophoretic separation medium, or the like. In another aspect, theoptical property is a fluorescence property, such as emission spectrum,fluorescence lifetime, fluorescence intensity at a given wavelength orband of wavelengths, or the like. Preferably, the fluorescence propertyis fluorescence intensity. For example, each molecular tag of aplurality may have the same fluorescent emission properties, but eachwill differ from one another by virtue of a unique retention time. Onthe other hand, or two or more of the molecular tags of a plurality mayhave identical migration, or retention, times, but they will have uniquefluorescent properties, e.g. spectrally resolvable emission spectra, sothat all the members of the plurality are distinguishable by thecombination of molecular separation and fluorescence measurement.

Preferably, released molecular tags are detected by electrophoreticseparation and the fluorescence of a detection group. In suchembodiments, molecular tags having substantially identical fluorescenceproperties have different electrophoretic mobilities so that distinctpeaks in an electropherogram are formed under separation conditions.Preferably, pluralities of molecular tags of the invention are separatedby conventional capillary electrophoresis apparatus, either in thepresence or absence of a conventional sieving matrix. Exemplarycapillary electrophoresis apparatus include Applied Biosystems (FosterCity, CA) models 310, 3100 and 3700; Beckman (Fullerton, CA) model P/ACEMDQ; Amersham Biosciences (Sunnyvale, CA) MegaBACE 1000 or 4000;SpectruMedix genetic analysis system; and the like. Electrophoreticmobility is proportional to q/M^(2/3), where q is the charge on themolecule and M is the mass of the molecule. Desirably, the difference inmobility under the conditions of the determination between the closestelectrophoretic labels will be at least about 0.001, usually 0.002, moreusually at least about 0.01, and may be 0.02 or more. Preferably, insuch conventional apparatus, the electrophoretic mobilities of moleculartags of a plurality differ by at least one percent, and more preferably,by at least a percentage in the range of from 1 to 10 percent. Moleculartags are identified and quantified by analysis of a separation profile,or more specifically, an electropherogram, and such values arecorrelated with the amounts and kinds of receptor dimers present in asample. For example, during or after electrophoretic separation, themolecular tags are detected or identified by recording fluorescencesignals and migration times (or migration distances) of the separatedcompounds, or by constructing a chart of relative fluorescent and orderof migration of the molecular tags (e.g., as an electropherogram).Preferably, the presence, absence, and/or amounts of molecular tags aremeasured by using one or more standards as disclosed by Williams et al,U.S. patent publication 2003/0170734A1, which is incorporated herein byreference.

Pluralities of molecular tags may also be designed for separation bychromatography based on one or more physical characteristics thatinclude but are not limited to molecular weight, shape, solubility, pKa,hydrophobicity, charge, polarity, or the like, e.g. as disclosed in U.S.patent publication 2003/0235832, which is incorporated by reference. Achromatographic separation technique is selected based on parameterssuch as column type, solid phase, mobile phase, and the like, followedby selection of a plurality of molecular tags that may be separated toform distinct peaks or bands in a single operation. Several factorsdetermine which HPLC technique is selected for use in the invention,including the number of molecular tags to be detected (i.e. the size ofthe plurality), the estimated quantities of each molecular tag that willbe generated in the assays, the availability and ease of synthesizingmolecular tags that are candidates for a set to be used in multiplexedassays, the detection modality employed, and the availability,robustness, cost, and ease of operation of HPLC instrumentation,columns, and solvents. Generally, columns and techniques are favoredthat are suitable for analyzing limited amounts of sample and thatprovide the highest resolution separations. Guidance for making suchselections can be found in the literature, e.g. Snyder et al, PracticalHPLC Method Development, (John Wiley & Sons, New York, 1988); Millner,“High Resolution Chromatography: A Practical Approach”, OxfordUniversity Press, New York (1999), Chi-San Wu, “Column Handbook for SizeExclusion Chromatography”, Academic Press, San Diego (1999), and Oliver,“HPLC of Macromolecules: A Practical Approach, Oxford University Press”,Oxford, England (1989). In particular, procedures are available forsystematic development and optimization of chromatographic separationsgiven conditions, such as column type, solid phase, and the like, e.g.Haber et al, J. Chromatogr. Sci., 38: 386-392 (2000); Outinen et al,Eur. J. Pharm. Sci., 6: 197-205 (1998); Lewis et al, J. Chromatogr.,592: 183-195 and 197- 208 (1992); and the like. An exemplary HPLCinstrumentation system suitable for use with the present invention isthe Agilent 1100 Series HPLC system (Agilent Technologies, Palo Alto,CA).

In one aspect, molecular tag, E, is (M, D), where M is amobility-modifying moiety and D is a detection moiety. The notation “(M,D)” is used to indicate that the ordering of the M and D moieties may besuch that either moiety can be adjacent to the cleavable linkage, L.That is, “B-L-(M, D)” designates binding compound of either of twoforms: “B-L-M-D” or “B-L-D-M.”

Detection moiety, D, may be a fluorescent label or dye, a chromogeniclabel or dye, an electrochemical label, or the like. Preferably, D is afluorescent dye. Exemplary fluorescent dyes for use with the inventioninclude water-soluble rhodamine dyes, fluoresceins,4,7-dichlorofluoresceins, benzoxanthene dyes, and energy transfer dyes,disclosed in the following references: Handbook of Molecular Probes andResearch Reagents, 8^(th) ed., (Molecular Probes, Eugene, 2002); Lee etal, U.S. patent 6,191,278; Lee et al, U.S. patent 6,372,907; Menchen etal, U.S. patent 6,096,723; Lee et al, U.S. patent 5,945,526; Lee et al,Nucleic Acids Research, 25: 2816-2822 (1997); Hobb, Jr., U.S. patent4,997,928; Khanna et al., U.S. patent 4,318,846; and the like.Preferably, D is a fluorescein or a fluorescein derivative.

In an embodiment illustrated in Fig. 3A, binding compounds comprise abiotinylated antibody (300) as a binding moiety. Molecular tags areattached to binding moiety (300) by way of avidin or streptavidin bridge(306). Preferably, in operation, binding moiety (300) is first reactedwith a target complex, after which avidin or streptavidin is added (304)to form antibody-biotin-avidin complex (305). To such complexes (305)are added (308) biotinylated molecular tags (310) to form bindingcompound (312).

In still another embodiment illustrated in Fig. 3B, binding compoundscomprise an antibody (314) derivatized with a multi-functional moiety(316) that contains multiple functional groups (318) that are reacted(320) molecular tag precursors to give a final binding compound havingmultiple molecular tags (322) attached. Exemplary multi-functionalmoieties include aminodextran, and like materials.

Once each of the binding compounds is separately derivatized by adifferent molecular tag, it is pooled with other binding compounds toform a plurality of binding compounds. Usually, each different kind ofbinding compound is present in a composition in the same proportion;however, proportions may be varied as a design choice so that one or asubset of particular binding compounds are present in greater or lowerproportion depending on the desirability or requirements for aparticular embodiment or assay. Factors that may affect such designchoices include, but are not limited to, antibody affinity and avidityfor a particular target, relative prevalence of a target, fluorescentcharacteristics of a detection moiety of a molecular tag, and the like.

B. Cleavage-Inducing Moiety Producing Active Species

A cleavage-inducing moiety, or cleaving agent, is a group that producesan active species that is capable of cleaving a cleavable linkage,preferably by oxidation. Preferably, the active species is a chemicalspecies that exhibits short-lived activity so that its cleavage-inducingeffects are only in the proximity of the site of its generation. Eitherthe active species is inherently short lived, so that it will not createsignificant background because beyond the proximity of its creation, ora scavenger is employed that efficiently scavenges the active species,so that it is not available to react with cleavable linkages beyond ashort distance from the site of its generation. Illustrative activespecies include singlet oxygen, hydrogen peroxide, NADH, and hydroxylradicals, phenoxy radical, superoxide, and the like. Illustrativequenchers for active species that cause oxidation include polyenes,carotenoids, vitamin E, vitamin C, amino acid-pyrrole N-conjugates oftyrosine, histidine, and glutathione, and the like, e.g. Beutner et al,Meth. Enzymol., 319: 226-241 (2000).

An important consideration in designing assays employing acleavage-inducing moiety and a cleavable linkage is that they not be sofar removed from one another when bound to a receptor complex that theactive species generated by the cleavage-inducing moiety cannotefficiently cleave the cleavable linkage. In one aspect, cleavablelinkages preferably are within 1000 nm, and preferably within 20-200 nm,of a bound cleavage-inducing moiety. More preferably, forphotosensitizer cleavage-inducing moieties generating singlet oxygen,cleavable linkages are within about 20-100 nm of a photosensitizer in areceptor complex. The range within which a cleavage-inducing moiety caneffectively cleave a cleavable linkage (that is, cleave enough moleculartag to generate a detectable signal) is referred to herein as its“effective proximity.” One of ordinary skill in the art recognizes thatthe effective proximity of a particular sensitizer may depend on thedetails of a particular assay design and may be determined or modifiedby routine experimentation.

A sensitizer is a compound that can be induced to generate a reactiveintermediate, or species, usually singlet oxygen. Preferably, asensitizer used in accordance with the invention is a photosensitizer.Other sensitizers included within the scope of the invention arecompounds that on excitation by heat, light, ionizing radiation, orchemical activation will release a molecule of singlet oxygen. The bestknown members of this class of compounds include the endoperoxides suchas 1,4-biscarboxyethyl-1,4-naphthalene endoperoxide,9,10-diphenylanthracene-9,10-endoperoxide and 5,6,11,12-tetraphenylnaphthalene 5,12-endoperoxide. Heating or direct absorption of light bythese compounds releases singlet oxygen. Further sensitizers aredisclosed in the following references: Di Mascio et al, FEBS Lett., 355:287 (1994)(peroxidases and oxygenases); Kanofsky, J.Biol. Chem. 258:5991-5993 (1983)(lactoperoxidase); Pierlot et al, Meth. Enzymol., 319:3-20 (2000)(thermal lysis of endoperoxides); and the like. Attachment ofa binding agent to the cleavage-inducing moiety may be direct orindirect, covalent or non-covalent and can be accomplished by well knowntechniques, commonly available in the literature. See, for example,“Immobilized Enzymes,” Ichiro Chibata, Halsted Press, New York (1978);Cuatrecasas, J. Biol. Chem., 245:3059 (1970).

As mentioned above, the preferred cleavage-inducing moiety in accordancewith the present invention is a photosensitizer that produces singletoxygen. As used herein, “photosensitizer” refers to a light-adsorbingmolecule that when activated by light converts molecular oxygen intosinglet oxygen. Photosensitizers may be attached directly or indirectly,via covalent or non-covalent linkages, to the binding agent of aclass-specific reagent. Guidance for constructiing of such compositions,particularly for antibodies as binding agents, available in theliterature, e.g. in the fields of photodynamic therapy,immunodiagnostics, and the like. The following are exemplary references:Ullman, et al., Proc. Natl. Acad. Sci. USA 91, 5426-5430 (1994); Stronget al, Ann. New York Acad. Sci., 745: 297-320 (1994); Yarmush et al,Crit. Rev. Therapeutic Drug Carrier Syst., 10: 197-252 (1993); Pease etal, U.S. patent 5,709,994; Ullman et al, U.S. patent 5,340,716; Ullmanet al, U.S. patent 6,251,581; McCapra, U.S. patent 5,516,636; and thelike.

A large variety of light sources are available to photo-activatephotosensitizers to generate singlet oxygen. Both polychromatic andmonchromatic sources may be used as long as the source is sufficientlyintense to produce enough singlet oxygen in a practical time duration.The length of the irradiation is dependent on the nature of thephotosensitizer, the nature of the cleavable linkage, the power of thesource of irradiation, and its distance from the sample, and so forth.In general, the period for irradiation may be less than about amicrosecond to as long as about 10 minutes, usually in the range ofabout one millisecond to about 60 seconds. The intensity and length ofirradiation should be sufficient to excite at least about 0.1% of thephotosensitizer molecules, usually at least about 30% of thephotosensitizer molecules and preferably, substantially all of thephotosensitizer molecules. Exemplary light sources include, by way ofillustration and not limitation, lasers such as, e.g., helium-neonlasers, argon lasers, YAG lasers, He/Cd lasers, and ruby lasers;photodiodes; mercury, sodium and xenon vapor lamps; incandescent lampssuch as, e.g., tungsten and tungsten/halogen; flashlamps; and the like.By way of example, a photoactivation device disclosed in Bjornson et al,International patent publication WO 03/051669 is employed. Briefly, thephotoactivation device is an array of light emitting diodes (LEDs)mounted in housing that permits the simultaneous illumination of all thewells in a 96-well plate. A suitable LED for use in the presentinvention is a high power GaAIAs IR emitter, such as model OD-880Wmanufactured by OPTO DIODE CORP. (Newbury Park, CA).

Examples of photosensitizers that may be utilized in the presentinvention are those that have the above properties and are enumerated inthe following references: Singh and Ullman, U.S. patent 5,536,834; Li etal, U.S. patent 5,763,602; Martin et al, Methods Enzymol., 186: 635-645(1990);Yarmush et al, Crit. Rev. Therapeutic Drug Carrier Syst., 10:197-252 (1993); Pease et al, U.S. patent 5,709,994; Ullman et al, U.S.patent 5,340,716; Ullman et al, U.S. patent 6,251,581; McCapra, U.S.patent 5,516,636; Thetford, European patent publ. 0484027; Sessler etal, SPIE, 1426: 318-329 (1991); Magda et al, U.S. patent 5,565,552;Roelant, U.S. patent 6,001,673; and the like.

As with sensitizers, in certain embodiments, a photosensitizer may beassociated with a solid phase support by being covalently ornon-covalently attached to the surface of the support or incorporatedinto the body of the support. In general, the photosensitizer isassociated with the support in an amount necessary to achieve thenecessary amount of singlet oxygen. Generally, the amount ofphotosensitizer is determined empirically.

In one embodiment, a photosensitizer is incorporated into a latexparticle to form photosensitizer beads, e.g. as disclosed by Pease etal., U.S. patent 5,709,994; Pollner, U.S. patent 6,346,384; and Pease etal, PCT publication WO 01/84157. Alternatively, photosensitizer beadsmay be prepared by covalently attaching a photosensitizer, such as rosebengal, to 0.5 micron latex beads by means of chloromethyl groups on thelatex to provide an ester linking group, as described in J. Amer. Chem.Soc., 97: 3741 (1975). Use of such photosensitizer beads is illustratedin Fig. 3C. As described in Fig. 1C for heteroduplex detection,complexes (330) are formed after combining reagents (1122) with asample. This reaction may be carried out, for example, in a conventional96-well or 384-well microtiter plate, or the like, having a filtermembrane that forms one wall, e.g. the bottom, of the wells that allowsreagents to be removed by the application of a vacuum. This allows theconvenient exchange of buffers, if the buffer required for specificbinding of binding compounds is different that the buffer required foreither singlet oxygen generation or separation. For example, in the caseof antibody-based binding compounds, a high salt buffer is required. Ifelectrophoretic separation of the released tags is employed, then betterperformance is achieved by exchanging the buffer for one that has alower salt concentration suitable for electrophoresis. In thisembodiment, instead of attaching a photosensitizer directly to a bindingcompound, such as an antibody, a cleaving probe comprises twocomponents: antibody (332) derivatized with a capture moiety, such asbiotin (indicated in Fig. 3C as “bio”) and photosensitizer bead (338)whose surface is derivatized with an agent (334) that specifically bindswith the capture moiety, such as avidin or streptavidin. Complexes (330)are then captured (335) by photosensitizer beads by way of the capturemoiety, such as biotin (336). Conveniently, if the pore diameter of thefilter membrane is selected so that photosensitizer beads (338) cannotpass, then a buffer exchange also serves to remove unbound bindingcompounds, which leads to an improved signal. After an appropriatebuffer for separation has been added, if necessary, photosensitizerbeads (338) are illuminated so that singlet oxygen is generated (342)and molecular tags are released (344). Such released molecular tags(346) are then separated to form separation profile (352) and dimers arequantified ratiometrically from peaks (348) and (350). Photosensitizerbeads may be used in either homogeneous or heterogeneous assay formats.

Preferably, when analytes, such as cell surface receptors, are beingdetected or antigen in a fixed sample, a cleaving probe may comprise aprimary haptenated antibody and a secondary anti-hapten binding proteinderivatized with multiple photosensitizer molecules. A preferred primaryhaptenated antibody is a biotinylated antibody, and preferred secondaryanti-hapten binding proteins may be either an anti-biotin antibody orstreptavidin. Other combinations of such primary and secondary reagentsare well known in the art, e.g. Haugland, Handbook of Fluorescent Probesand Research Reagents, Ninth Edition (Molecular Probes, Eugene, OR,2002). An exemplary combination of such reagents is illustrated in Fig.3E. There binding compounds (366 and 368) having releasable tags (“mT₁”and “mT₂” in the Figure), and primary antibody (368) derivatized withbiotin (369) are specifically bound to different epitopes of receptordimer (362) in membrane (360). Biotin-specific binding protein (370),e.g. streptavidin, is attached to biotin (369) bringing multiplephotosensitizers (372) into effective proximity of binding compounds(366 and 368). Biotin-specific binding protein (370) may also be ananti-biotin antibody, and photosensitizers may be attached via freeamine group on the protein by conventional coupling chemistries, e.g.Hermanson (cited above). An exemplary photosensitizer for such use is anNHS ester of methylene blue prepared as disclosed in Shimadzu et al,European patent publication 0510688.

Assay Conditions

The following general discussion of methods and specific conditions andmaterials are by way of illustration and not limitation. One of ordinaryskill in the art will understand how the methods described herein can beadapted to other applications, particularly with using differentsamples, cell types and target complexes.

In conducting the methods of the invention, a combination of the assaycomponents is made, including the sample being tested, the bindingcompounds, and optionally the cleaving probe. Generally, assaycomponents may be combined in any order. In certain applications,however, the order of addition may be relevant. For example, one maywish to monitor competitive binding, such as in a quantitative assay. Orone may wish to monitor the stability of an assembled complex. In suchapplications, reactions may be assembled in stages, and may requireincubations before the complete mixture has been assembled, or beforethe cleaving reaction is initiated.

The amounts of each reagent are usually determined empirically. Theamount of sample used in an assay will be determined by the predictednumber of target complexes present and the means of separation anddetection used to monitor the signal of the assay. In general, theamounts of the binding compounds and the cleaving probe are provided inmolar excess relative to the expected amount of the target molecules inthe sample, generally at a molar excess of at least 1.5, more desirablyabout 10-fold excess, or more. In specific applications, theconcentration used may be higher or lower, depending on the affinity ofthe binding agents and the expected number of target molecules presenton a single cell. Where one is determining the effect of a chemicalcompound on formation of oligomeric cell surface complexes, the compoundmay be added to the cells prior to, simultaneously with, or afteraddition of the probes, depending on the effect being monitored.

The assay mixture is combined and incubated under conditions thatprovide for binding of the probes to the cell surface molecules, usuallyin an aqueous medium, generally at a physiological pH (comparable to thepH at which the cells are cultures), maintained by a buffer at aconcentration in the range of about 10 to 200 mM. Conventional buffersmay be used, as well as other conventional additives as necessary, suchas salts, growth medium, stabilizers, etc. Physiological and constanttemperatures are normally employed. Incubation temperatures normallyrange from about 4 degrees to 70 degrees C, usually from about 15degrees to 45 degrees C, more usually 25 degrees to 37 degrees .

After assembly of the assay mixture and incubation to allow the probesto bind to cell surface molecules, the mixture is treated to activatethe cleaving agent to cleave the tags from the binding compounds thatare within the effective proximity of the cleaving agent, releasing thecorresponding tag from the cell surface into solution. The nature ofthis treatment will depend on the mechanism of action of the cleavingagent. For example, where a photosensitizer is employed as the cleavingagent, activation of cleavage will comprise irradiation of the mixtureat the wavelength of light appropriate to the particular sensitizerused.

Following cleavage, the sample is then analyzed to determine theidentity of tags that have been released. Where an assay employing aplurality of binding compounds is employed, separation of the releasedtags will generally precede their detection. The methods for bothseparation and detection are determined in the process of designing thetags for the assay. A preferred mode of separation employselectrophoresis, in which the various tags are separated based on knowndifferences in their electrophoretic mobilities.

As mentioned above, in some embodiments, if the assay reactionconditions may interfere with the separation technique employed, it maybe necessary to remove, or exchange, the assay reaction buffer prior tocleavage and separation of the molecular tags. For example, assayconditions may include salt concentrations (e.g. required for specificbinding) that degrade separation performance when molecular tags areseparated on the basis of electrophoretic mobility. Thus, such high saltbuffers may be removed, e.g. prior to cleavage of molecular tags, andreplaced with another buffer suitable for electrophoretic separationthrough filtration, aspiration, dilution, or other means.

EXAMPLES

Sources of Materials Used in Examples

Antibodies specific for Her receptors, adaptor molecules, andnormalization standards are obtained from commercial vendors, includingLabvision, Cell Signaling Technology, and BD Biosciences. All cell lineswere purchased from ATCC. All human snap-frozen tissue samples werepurchased from either William Bainbridge Genome Foundation (Seattle, WA)or Bio Research Support (Boca Raton, FL) and were approved byInstitutional Research Board (IRB) at the supplier.

The molecular tag-antibody conjugates used below are formed by reactingNHS esters of the molecular tag with a free amine on the indicatedantibody using conventional procedures. Molecular tags, identified belowby their “Pro_N” designations, are disclosed in the followingreferences: Singh et al, U.S. patent publications, 2003/017915 and2002/0013126, which are incorporated by reference. Briefly, bindingcompounds below are molecular tag-monoclonal antibody conjugates formedby reacting an NHS ester of a molecular tag with free amines of theantibodies in a conventional reaction.

Example 1:Analysis of Cell Lysates for Her-2 Heterodimerization andReceptor Phosphorylation

In this example, Her1-Her2 and Her2-Her3 heterodimers andphosphorylation states are measured in cell lysates from several celllines after treatment with various concentrations of epidermal growthfactor (EGF) and heregulin (HRG). Measurements are made using threebinding compounds and a cleaving probe as described below.

Sample Preparation:

Serum-starve breast cancer cell line culture overnight before use.

-   Stimulate cell lines with EGF and/or HRG in culture media for 10    minutes at 37 degrees C. Exemplary doses of EGF/HRG are 0, 0.032,    0.16, 0.8, 4, 20, 100 nM for all cell lines (e.g. MCF-7, T47D,    SKBR-3) except BT20 for which the maximal dose is increased to 500    nM because saturation is not achieved with 100 nM EGF.-   Aspirate culture media, transfer onto ice, and add lysis buffer to    lyse cells in situ.-   Scrape and transfer lysate to microfuge tube. Incubate on ice for 30    min. Microfuge at 14,000 rpm, 4 degrees C, for 10 min.    (Centrifugation is optional.)-   Collect supernatants as lysates and aliquot for storage at –80    degrees C until use.

Assay:

Assay design: As illustrated diagrammatically in Fig. 4A, Her2-Her3heterodimers (900) are quantified ratiometrically based on the bindingof cleaving probe (902) and binding compounds (904), (906), and (908). Aphotosensitizer indicated by “PS” is attached to cleaving probe (902)via an avidin-biotin linkage, and binding compounds (904), (906), and(908) are labeled with molecular tags Pro14, Pro10, and Pro11,respectively. Binding compound (904) is specific for a phosphorylationsite on Her3.

The total assay volume is 40 ul. The lysate volume is adjusted to 30 ulwith lysis buffer. The antibodies are diluted in lysis buffer up to10ul. Typically about 5000 to 15000 cell-equivalent of lysates is usedper reaction. The detection limit is about 1000 cell-equivalent oflysates.

Procedure: Final concentrations of pre-mixed binding compounds (i.e.molecular tag- or biotin-antibody conjugates) in reaction:Pro4_anti-Her-2: 0.1ug/ml Pro10_anti-Her-1: 0.05-0.1 ug/mlPro11_anti-Her-3: 0.1 ug/ml Pro2_anti-phospho-Tyr: 0.1 ug/mlBiotin_anti-Her-2: 1-2 ug/ml To assay 96-well, add 10 ul antibody mix to30 ul lysate and incubate for 1 hour at RT. Add 2 ulstreptavidin-derivatized cleaving probe (final 2 ug/well) to assay welland incubate for 45 min. Add 150 ul of PBS with 1% BSA to 96-well filterplate (Millipore MAGVN2250) and incubate for 1 hr at RT for blocking.Empty filter plate by vacuum suction. Transfer assay reactions to filterplate and apply vacuum to empty. Add 200 ul wash buffer and apply vacuumto empty. Repeat one time. Add 200 ul illumination buffer and applyvacuum to empty. Repeat one time. Add 30 ul illumination buffer andilluminate for 20 min. Transfer 10 ul of each reaction to CE assay platefor analysis using an ABI3100 CE instrument with a 22 cm capillary(injection conditions: 5 kV, 75 sec, 30 degrees C; run conditions: 600sec, 30 degrees C).

Assay buffers are as follows:

Lysis Buffer (made fresh and stored on ice) Final ul Stock 1% TritonX-100 1000 10% 20 mM Tris-HCl (pH 7.5) 200 1 M 100 mM NaCl 200 5 M 50 mMNaF 500 1 M 50 mM Na beta-glycerophosphate 1000 0.5 M 1 mM Na₃VO₄ 1000.1 M 5 mM EDTA 100 0.5 M 10 ug/ml pepstatin 100 1 mg/ml 1 tablet (per10 ml) Roche Complete protease inhibitor (No. 1836170) N/A N/A Water6500 N/A 10 ml Total Wash buffer (stored at 4 degrees C) Final ml Stock1% NP-40 50 10% 1x PBS 50 10x 150 mM NaCl 15 5 M 5 mM EDTA 5 0.5 M Water380 N/A 500 ml Total Illumination buffer: Final ul Stock 0.005x PBS 501x CE std 3 100x 10 mM Tris-HCl (pH 8.0) 0.1M 10 pM A160 1 nM 10 pM A3151 nM 10 pM HABA 1 nM Water 10,000 N/A 10 ml Total

Data Analysis: Normalize relative fluorescence units (RFU) signal ofeach molecular tag against CE reference standard A315 (afluorescein-derivatized deoxyadenosine monophosphate that has known peakposition relative to molecular tags from the assay upon electrophoreticseparation). Subtract RFU of “no lysate” background control fromcorresponding molecular tag signals. Report heterodimerization for Her-1or Her-3 as the corresponding RFU ratiometric to RFU fromPro4_anti-Her-2 from assay wells using biotin-anti-Her-2. Reportreceptor phosphorylation for Her-1,2,3 as RFU from Pro2_PT100anti-phospho-Tyr ratiometric to RFU from Pro4_anti-Her-2 from assaywells using biotin-anti-Her-2. Results of the assays are illustrated inFigs. 4B-4H. Fig. 4B shows the quantity of Her1-Her2 heterodimersincreases on MCF-7 cells with increasing concentrations of EGF, whilethe quantity of the same dimer show essentially no change withincreasing concentrations of HRG. Fig. 4C shows the opposite result forHer2-Her3 heterodimers. That is, the quantity of Her2-Her3 heterodimersincreases on MCF-7 cells with increasing concentrations of HRG, whilethe quantity of the same dimer show essentially no change withincreasing concentrations of EGF. Figs. 4D and 4E show the quantity ofHer1-Her2 heterodimers increases on SKBR-3 cells and BT-20 cells,respectively, with increasing concentrations of EGF.

Example 2:Analysis of Tissue Lysates for Her2 Heterodimerization andReceptor Phosphorylation

In this example, Her1-Her2 and Her2-Her3 heterodimers andphosphorylation states are measured in tissue lysates from human breastcancer specimens.

Sample Preparation: Snap frozen tissues are mechanically disrupted atthe frozen state by cutting. Transfer tissues to microfuge tube and add3x tissue volumes of lysis buffer (from appendix I) followed byvortexing to disperse tissues in buffer. Incubate on ice for 30 min withintermittent vortexing to mix. Centrifuge at 14,000 rpm, 4 degrees C,for 20 min. Collect supernatants as lysates and determine total proteinconcentration with BCA assay (Pierce) using a small aliquot. Aliquot therest for storage at –80 degrees C until use.

Assay design: The total assay volume is 40 ul. The lysates are tested inserial titration series of 40, 20, 10, 5, 2.5, 1.25, 0.63, 0.31 ugtotal-equivalents and the volume is adjusted to 30 ul with lysis buffer.Data from the titration series confirm the specificity of thedimerization or phosphorylation signals. A universal antibody mixcomprising all eTag-antibodies diluted in lysis buffer is used at thefollowing concentrations. Individual biotin-antibody for each receptoris added separately to the reactions. Three eTag assays are conductedwith each tissue lysate, each using a different biotin-antibodycorresponding to specific receptor dimerization to be measured.Expression level of each receptor is determined from different assaycontaining the biotin-antibody specific to the receptor. Dimerizationand phosphorylation signals are determined ratiometrically only in theassay containing the biotin-anti-Her-2.

Assay controls: MCF-10A and MCF-7 cell lines are used as qualitativenegative and positive controls, respectively. Cell lines are eitherunstimulated or stimulated with 100 nM EGF or 100 nM HRG. Lysis bufferis included as a background control when replacing the tissue samples.

Final concentrations of pre-mixed antibodies in reactions: Universalantibody mix: Pro4_anti-Her-2: 0.1ug/ml Pro10_anti-Her-1: 0.05 ug/mlPro11_anti-Her-3: 0.1 ug/ml Pro2_anti-phospho-Tyr: 0.01 ug/ml Individualbiotin antibody: Biotin_anti-Her-1: 2 ug/ml Biotin_anti-Her-2: 2 ug/mlBiotin_anti-Her-3: 2 ug/ml

Procedure: Prepare antibody reaction mix by adding biotin antibody touniversal antibody mix. To assay 96-well, add 10 ul universal reactionmix to 30 ul lysate and incubate for 1 hour at RT. Add 2 ulstreptavidin-derivatized cleaving probe (final 2 ug/well) to assay welland incubate for 45 min. Add 150 ul of PBS with 1% BSA to 96-well filterplate (Millipore MAGVN2250) and incubate for 1 hr at RT for blocking.Empty filter plate by vacuum suction. Transfer assay reactions to filterplate and apply vacuum to empty. Add 200 ul wash buffer and apply vacuumto empty. Repeat one time. Add 200 ul illumination buffer and applyvacuum to empty. Repeat one time. Add 30 ul illumination buffer andilluminate for 20 min. Transfer 10 ul of each reaction to CE assay platefor analysis using ABI3100 capillary electrophoresis instrument with a22 cm capillary (injection conditions: 5 kV, 75 sec, 30 degrees C; runconditions: 600 sec, 30 degrees C)

Data Analysis:

-   Normalize RFU signal of each molecular tag against CE reference    standard A315.-   Determine the cut-off values of RFU (each for dimerization or    phosphorylation) below which ratios are not calculated because the    signals are too low to be reliable. Below the cut-off values, the    RFU signals are not titratable in the series of lysate dilution    tested. The values can be determined with a large set of normal    tissues where dimerization and phosphorylation signals are expected    to be absent or at the lowest. These values also represent the basal    level of dimerization or phosphorylation on the normal tissues to    which tumor tissues will be compared.-   For the minority of normal tissues, if present, with RFU values    above the cut-off, determine the individual RFU level and    ratiometric readouts of Her-1 or Her-3 heterodimerization or    phosphorylation peaks detected. These samples represent outliers    that should be used as matched donor controls for the corresponding    tumor tissue samples while scoring.-   For all tumor samples showing titratable RFU signals, use the lowest    signal of each of Her-1, Her-2, Her-3, or phosphorylation from the    tissue lysate titration series as the background. Subtract this    background from the molecular tag signals of the high dose lysates    (e.g. 40 ug) to yield the specific RFU signals. If there is no    signal dose response in the titration series, all signals (which are    usually very low) are considered background and no specific signals    can be used for ratiometric analysis.-   Report heterodimerization for Her-1 or Her-3 as the corresponding    specific RFU ratiometric to the specific RFU from Pro4_anti-Her-2.    If no specific RFU is obtained, the dimerization is negative.-   Report receptor phosphorylation for Her-1,2,3 as specific RFU from    Pro2_anti-phospho-Tyr ratiometric to the specific RFU from    Pro4_anti-Her-2. If no specific RFU is obtained, the phosphorylation    is negative.

In Figs. 5A-5C data shown are representative of multiple patients’breast tissue samples tested with assays of the invention. The clinicalHer-2 status from immunohistochemistry (DAKO Herceptest) of 9 out of 10tumor samples was negative, indicative of either undetectable Her-2staining, or staining of less than 10% of the tumor cells, or a faintand barely perceptible staining on part of the cell membrane of morethan 10% tumor cells. The assays of the invention determined theexpression of Her-1, Her-2, and Her-3 on both normal and tumor tissues.The heterodimerization of Her1 and Her2 and of Her2 and Her3 wasdetected only in tumor tissues but not in any normal tissues.

Example 3: Analysis of Cell Lysates for Her1 or Her2 Homodimerizationand Receptor Phosphorylation

Sample preparation was carried out essentially as described in Example2. Her1 homodimerization was induced by treating the cell lines with EGFor TGF alpha. For homodimerization of Her2 which does not have a ligand,unstimulated SKBR-3 or MDA-MD-453 cells that overexpress Her2 arecompared to unstimulated MCF-7 cells that express a low level of Her2.

Assay design: A monoclonal antibody specific to the receptor isseparately conjugated with either a molecular tag or biotin (that isthen linked to a photosensitizer via an avidin bridge), so that thecleaving probe and a binding compound compete to bind to the sameepitope in this example. Another binding compound is used that consistsof a second anibody recognizing an overlapping epitope on the receptor,so that a ratiometric signal can be generated as a measure ofhomodimerization. The signal derived from the second antibody alsoprovides a measure of the total amount of receptor in a sample. Thetotal amount of receptor is determined in a separate assay well.Receptor phosphorylation can be quantified together with eitherhomodimerization or total receptor amount.

Procedure: The assay volume is 40 ul and the general procedure issimilar to that of Example 2. Two assay wells, A and B, are set up foreach sample to quantify homodimerization and total amount of receptorseparately.

For quantification of Her1-Her1 homodimers: Final concentrations inantibody mix in assay well A: Pro12_anti-Her-1: 0.05-0.1 ug/mlBiotin_anti-Her-1: 1-2 ug/ml Final concentrations in antibody mix inassay well B: Pro10_anti-Her-1: 0.05-0.1 ug/ml Pro2_anti-phospho-Tyr:0.1 ug/ml Biotin_anti-Her-1: 1-2 ug/ml

For quantification of Her2-Her2 homodimers: Final concentrations inantibody mix in assay well A: Pro4_anti-Her-1: 0.05-0.1 ug/mlBiotin_anti-Her-1: 1-2 ug/ml Final concentrations in antibody mix inassay well B: Pro4_anti-Her-1: 0.05-0.1 ug/ml Pro2_anti-phospho-Tyr: 0.1ug/ml Biotin_anti-Her-1: 1-2 ug/ml

Data Analysis:

-   Normalize RFU signal of each molecular tag against CE reference    standard A315.-   Subtract RFU of “no lysate” background control from corresponding    molecular tag signals.-   Report homodimerization for Her-1 or Her-2 as the corresponding    normalized RFU from assay well A as ratiometric to normalized RFU of    total receptor amount from the corresponding assay well B.-   Report receptor phosphorylation for Her-1 or Her-2 homodimer as    normalized RFU from Pro2_PT100 anti-phospho-Tyr from assay well B as    ratiometric to normalized RFU from total receptor amount from the    same assay well B.

Results of the assays are illustrated in Figs. 6A-6B and Fig. 7. Fig. 6Ashows that the quantity of Her1-Her1 homodimers on BT-20 cells increaseswith increasing concentration of EGF. Fig. 6B shows that the quantity ofHer1 phosphorylation in BT-20 cells increases with increasing EGFconcentration. The detection of Her2-Her2 homodimers was demonstrated bycomparison of signals from SKBR-3 cells expressing Her2 with signalsfrom MCF-7 cells that express reduced level of Her2 on the cell surface.As shown in the charts of Fig. 7, no specific titratable Her2-Her2homodimer signals were detected with MCF-7 cells whereas Her2-Her2homodimer signals from SKBR-3 cells were clearly above the signals fromMCF-7 cells.

Example 4: Analysis of Cell Lysates for Her1-Her3 Heterodimerization andReceptor Phosphorylation

Samples are prepared as follows: 1. Serum-starve breast cancer cell lineculture overnight before use. 2. Stimulate cell lines with HRG inculture media for 10 minutes at 37 degrees C. Exemplary doses of HRG are0, 0.032, 0.16, 0.8, 4, 20, 100 nM for T47D cells. 3. Aspirate culturemedia, transfer onto ice, and add lysis buffer to lyse cells in situ. 4.Scrape and transfer lysate to microfuge tube. Incubate on ice for 30min. Microfuge at 14,000 rpm, 4 degrees C, for 10 min. (Centrifugationis optional.) 5. Collect supernatants as lysates and aliquot for storageat –80 degrees C until use.

Assay design: The total assay volume is 40 ul. The lysate volume isadjusted to 30 ul with lysis buffer. The antibodies are diluted in lysisbuffer up to 5 ul. Typically about 5000 to 50000 cell-equivalent oflysates is used per reaction. Final concentrations of pre-mixedantibodies in reaction: Pro10_anti-Her-1: 0.05-0.1 ug/mlPro11_anti-Her-3: 0.1 ug/ml Pro2_anti-phospho-Tyr: 0.1 ug/mlBiotin_anti-Her-3: 1-2 ug/ml 1. To assay 96-well, add 5 ul antibody mixto 30 ul lysate and incubate for 1 hour at RT. 2. Add 5 ulstreptavidin-derivatized molecular scissor (final 4 ug/well) to assaywell and incubate for 45 min. 3. Add 150 ul of PBS with 1% BSA to96-well filter plate (Millipore MAGVN2250) and incubate for 1 hr at RTfor blocking. 4. Empty filter plate by vacuum suction. Transfer assayreactions to filter plate and apply vacuum to empty. 5. Add 200 ul washbuffer and apply vacuum to empty. Repeat one time. 6. Add 200 ulillumination buffer and apply vacuum to empty. Repeat one time. 7. Add30 ul illumination buffer and illuminate for 20 min. 8. Transfer 10 ulof each reaction to CE assay plate for analysis using ABI3100 capillaryelectrophoresis instrument with a 22 cm capillary (injection conditions:5 kV, 425 sec, 30 degrees C; run conditions: 600 sec, 30 degrees C).

Data Analysis:

-   1. Normalize RFU signal of each eTag reporter against CE reference    standard A315.-   2. Subtract RFU of “no lysate” background control from corresponding    eTag reporter signals.-   3. Report heterodimerization as the Her-1 derived Pro10 RFU    ratiometric to Pro11 RFU from anti-Her-3.-   4. Report receptor phosphorylation for Her-1/3 as RFU from    Pro2_PT100 anti-phospho-Tyr ratiometric to RFU from Pro11_anti-Her-3    from assay wells using biotin-anti-Her-3.

Results of the assay are illustrated in Figs. 8A and 8B. The data showthat both Her1-Her3 heterodimerization and dimer phosphorylationincrease with increasing concentrations of HRG.

Example 5: Increase in Her1-Her3 Receptor Dimer Expression in CancerCell Lines in Response to Increase in Epidermal Growth Factor

In this example, Her1-Her3 heterodimers are measured in cell lysatesfrom cancer cell lines 22Rv1 and A549 after treatment with variousconcentrations of epidermal growth factor (EGF). Measurements are madeusing three binding compounds and a cleaving probe as described below.

Sample Preparation: 1. Serum-starve breast cancer cell line cultureovernight before use. 2. Stimulate cell lines with EGF in culture mediafor 10 minutes at 37 degrees C. Exemplary doses of EGF applied to bothcell lines varied between 0-100 nM. 3. Aspirate culture media, transferonto ice, and add lysis buffer to lyse cells in situ. 4. Scrape andtransfer lysate to microfuge tube. Incubate on ice for 30 min. Microfugeat 14,000 rpm, 4 degrees C, for 10 min. (Centrifugation is optional.)Determine protein concentration. 5. Collect supernatants as lysates andaliquot for storage at –80 degrees C until use.

The assay design is essentially the same as illustrated in Fig. 4A, withthe following exceptions: binding compounds (904), (906), and (908) arelabeled with molecular tags Pro10, Pro11, and Pro 2, respectively. Thetotal assay volume is 40 ul. The lysate volume is adjusted to 30 ul withlysis buffer. The antibodies are diluted in lysis buffer up to 5ul.Typically about 5000 to 15000 cell-equivalent of lysates is used perreaction. The detection limit is about 1000 cell-equivalent of lysates.

Procedure: Final concentrations of pre-mixed binding compounds (i.e.molecular tag- or biotin-antibody conjugates) in reaction:Pro10_anti-Her-1: 0.05-0.1 ug/ml Pro11_anti-Her-3: 0.1 ug/mlPro2_anti-phospho-Tyr: 0.1 to 0.2 ug/ml Biotin_anti-Her-3: 1-2 ug/ml 1.To assay 96-well, add 5 ul antibody mix to 30 ul lysate and incubate for1 hour at RT. 2. Add 5 ul streptavidin-derivatized cleaving probe (final4 ug/well) to assay well and incubate for 45 min. 3. Add 150 ul of PBSwith 1% BSA to 96-well filter plate (Millipore MAGVN2250) and incubatefor 1 hr at RT for blocking. 4. Empty filter plate by vacuum suction.Transfer assay reactions to filter plate and apply vacuum to empty. 5.Add 200 ul wash buffer and apply vacuum to empty. Repeat one time. 6.Add 200 ul illumination buffer and apply vacuum to empty. Repeat onetime. 7. Add 30 ul illumination buffer and illuminate for 20 min. 8.Transfer 10 ul of each reaction to CE assay plate for analysis using anABI3100 CE instrument with a 22 cm capillary (injection conditions: 5kV, 70 sec, 30 degrees C; run conditions: 425 sec, 30 degrees C).

Assay buffers are as follows: Lysis Buffer (made fresh and stored onice) Final ul Stock 1% Triton X-100 1000 10% 20 mM Tris-HCl (pH 7.5) 5001 M 100 mM NaCl 200 5 M 50 mM NaF 500 1 M 50 mM Na beta-glycerophosphate500 1.0 M 1 mM Na₃VO₄ 100 0.1 M 5 mM EDTA 100 0.5 M 10 ug/ml pepstatin100 1 mg/ml 1 tablet (per 10 ml) Roche Complete protease inhibitor (No.1836170) N/A N/A Water 7 ml N/A 10 ml Total Wash buffer (stored at 4degrees C): 0.5% Triton X100 in 1x PBS. Illumination buffer: Final ulStock 0.005x PBS 50 1x CE std 1 (A27, ACLARA Biosciences, Inc., MountainView, CA) 4 5000x CE std 2 (fluorescein) 4 5000x Water 9942 N/A 10 mlTotal

Data Analysis: 1. Normalize relative fluorescence units (RFU) signal ofeach molecular tag against CE reference standard 2. 2. Subtract RFU of“no lysate” background control from corresponding molecular tag signals.3. Report heterodimerization for Her-1 as the corresponding RFUratiometric to RFU from Pro11_anti-Her-3 from assay wells usingbiotin-anti-Her-3. 4. Report receptor phosphorylation for Her-1,2,3 asRFU from Pro2_PT100 anti-phospho-Tyr ratiometric to RFU fromPro11_anti-Her-3 from assay wells using biotin-anti-Her-3 (data notshown).

Fig. 9A and 9B show the increases in the numbers of Her1-Her3heterodimers on 22Rv1 and A549 cells, respectively, with increasingconcentrations of EGF.

Example 6: Occurrence of IGF-1R Heterodimers with Her1, Her2, and Her3in Breast Tumor Tissue Lysates

In this example, cells from 12 different human breast tumor tissues wereassayed for the presence of Her1-IGF-1R, Her2-IGF-1R, and Her3-IGF-1Rdimers using assays essentially the same as that illustrated in Fig. 4A.Sample Preparation was carried out as follows: 1. Snap frozen tissuesare mechanically disrupted at the frozen state by cutting. 2. Transfertissues to microfuge tube and add 3x tissue volumes of lysis bufferfollowed by vortexing to disperse tissues in buffer. 3. Incubate on icefor 30 min with intermittent vortexing to mix. 4. Centrifuge at 14,000rpm, 4 degrees C, for 20 min. 5. Collect supernatants as lysates anddetermine total protein concentration with BCA assay (Pierce) using asmall aliquot. 6. Aliquot the rest for storage at –80 degrees C untiluse.

The assay was set up as follows. 1. The total assay volume is 40 ul. 2.The lysates are tested in serial titration series of 40, 20, 10, 5, 2.5,1.25, 0.63, 0.31 ug total-equivalents and the volume is adjusted to 30ul with lysis buffer. Data from the titration series confirm thespecificity of the dimerization. 3. A universal antibody mix comprisingof all binding compounds and biotin antibody diluted in lysis buffer isused at concentrations given below.

Final concentrations of pre-mixed antibodies in reactions:Pro10_anti-Her-2: 0.1ug/ml Pro14_anti-Her-1: 0.1 ug/ml Pro11_anti-Her-3: 0.1 ug/ml Pro7_anti-IGF-1R: 0.1 ug/ml Pro2_anti-phospho-Tyr:0.2 ug/ml Biotin_anti-Her-2: 2 ug/ml

Procedure: 1. To assay 96-wells, add 5 ul universal reaction mix to 30ul lysate and incubate for 1 hour at RT. 2. Add 5 ulstrepatvidin-derivatized molecular scissor, i.e. cleaving probe (final 4ug/well) to assay well and incubate for 45 min. 3. Add 150 ul of of PBSwith 1% BSA to 96-well filter plate (Millipore MAGVN2250) and incubatefor 1 hr at RT for blocking. 4. Empty filter plate by vacuum suction.Transfer assay reactions to filter plate and apply vacuum to empty. 5.Add 200 ul wash buffer and apply vacuum to empty. Repeat one time. 6.Add 200 ul illumination buffer and apply vacuum to empty. Repeat onetime. 7. Add 30 ul illumination buffer and illuminate for 20 min. 8.Transfer 10 ul of each reaction to CE assay plate for analysis using:(i) CE equipment: ABI3100, 22 cm capillary, (ii) CE injectionconditions: 5 kV, 70 sec, 30 degrees C, and (iii) CE run conditions: 425sec, 30 degrees C.

Data Analysis: 1. Normalize RFU signal of each molecular tag against CEreference standard 1. 2. Look for titratable signals for each moleculartag. Signals that do not titrate are assumed to be non-specific signalsand are not used for data interpretation. A cut off value is determinedbased on the values from a large set of normal tissues wheredimerization signals are expected to be absent or at the lowest. Thesevalues also represent the basal level of dimerization on the normaltissues to which tumor tissues are compared. 3. Heterodimerization isreported for IGF-1R with Her-1 or Her-2 or Her-3 as the correspondingspecific RFU.

Two out of the twelve breast tumors assayed expressed Her1-IGF-1R,Her2-IGF-1R, and Her3-IGF-1R heterodimers, as shown in Figs. 10A-C. Thelines in each figure panel shows the trend between receptor heterodimerquantity measured and amount of lysate assayed for the two breast tumorsamples that were positive for the indicated heterodimers.

Example 7: PI3K/Her-3 Receptor Activation Complex

In this example, assays were designed as shown in Figs. 11A and 11C tomeasure a receptor complex comprising Her2, Her3, and PI3K in breastcancer cell line, MCF-7. Binding compound (1106) having a firstmolecular tag (“mT₁” in the figure and “eTag1” below) is specific forthe extracellular domain of Her3 receptor (1102), binding compound(1110) having a second molecular tag (“mT2” in the figure and “eTag2”below) is specific for the p185 component (1111) of PI3K protein (1100),and cleaving probe (1108) having a photosensitizer attached ( isspecific for the intracellular domain of Her3 receptor (1102) where “H2”indicates a Her2 receptor (1104), “H3” indicates a Her3 receptor (1102),“p85” and “p110” are components of PI3 kinase (1100), which binds to aphosphorylation site of H3 (denoted by “P”) through its p85 moiety. Thetwo assay designs are similar, except that in the design of Fig. 11A thecleaving probe is specific for the Her3 receptor, and in the design ofFig. 11C, the cleaving probe is specific for the p85 component of PI3kinase. The assays were carried out as follows.

Sample Preparation: 1. Serum-starve breast cancer cell line cultureovernight before use. 2. Stimulate cell lines with HRG in culture mediafor 10 minutes at 37 degrees C. Exemplary doses of HRG are 0, 0.032,0.16, 0.8, 4, 20, 100 nM for MCF-7 cells. 3. Aspirate culture media,transfer onto ice, and add lysis buffer (described above to lyse cellsin situ. 4. Scrape and transfer lysate to microfuge tube. Incubate onice for 30 min. Microfuge at 14,000 rpm, 4 degrees C, for 10 min. 5.Collect supernatants as lysates and aliquot for storage at –80 degrees Cuntil use.

Lysis Buffer (made fresh and stored on ice): Final ul Stock 1% TritonX-100 1000 10% 20 mM Tris-HCl (pH 7.5) 200 1 M 100 mM NaCl 200 5 M 50 mMNaF 500 1 M 50 mM Na beta-glycerophosphate 1000 0.5 M 1 mM Na₃VO₄ 1000.1 M 5 mM EDTA 100 0.5 M 10 ug/ml pepstatin 100 1 mg/ml 1 tablet (per10 ml) Roche Complete protease inhibitor (No. 1836170) N/A N/A Water6500 N/A 10 ml Total

Assay design: Receptor complex formation is quantified ratiometricallybased on the schematics illustrated in each figure. That is, the readoutof the assays are the peak ratios of molecular tags, eTag2/eTag1.

The total assay volume is 40 ul. The lysate volume is adjusted to 10 ulwith lysis buffer. The antibodies are diluted in lysis buffer up to 20ul. Typically about 5000 to 500,000 cell-equivalent of lysates is usedper reaction.

Procedure: Working concentrations of pre-mixed antibodies prior toadding into reaction: For Her-3/PI3K complex with cleaving probe atHer-3 (the design of Fig. 11A): eTag1_anti-Her-3 at 10 nM (eTag1 wasPro14 in this assay) eTag2_anti-PI3K at 10 nM (eTag2 was Pro1 in thisassay) Biotin_anti-Her-3 at 20 nM Universal Standard US-1 at 700 nM TheUniversal Standard US-1 is BSA conjugated with biotin and molecular tagPro8, which is used to normalize the amount ofstreptavidin-photosensitizer beads in an assay. The molecular tags wereattached directly to antibodies by reacting an NHS-ester of a moleculartag precursor with free amines on the antibodies using conventionaltechniques, e.g. Hermanson (cited above).

For Her-3/PI3K complex with cleaving probe at PI3K (the design of Fig.11C): eTag1_anti-PI3K at 10 nM (eTag1 was Pro1 in this assay)eTag2_anti-Her-3 at 10 nM (eTag2 was Pro14 in this assay)Biotin_anti-PI3K at 20 nM Universal Standard US-1 at 700 nM To assay96-well filter plate (Millipore MAGVN2250), add 20 ul antibody mix to 10ul lysate and incubate for 1 hour at 4 degrees C. Add 10 ulstreptavidin-derivatized cleaving probe (final 4 ug/well) to assay welland incubate for 40 min. Add 200 ul wash buffer and apply vacuum toempty. Add 30 ul illumination buffer and illuminate. Transfer 10 ul ofeach reaction to CE assay plate for analysis.

Data Analysis: 1. Normalize relative fluorescence units (RFU) signal ofeach molecular tag against that of internal Universal Standard US-1. 2.Subtract RFU of “no lysate” background control from correspondingnormalized eTag reporter signals. 3. Report receptor complex formationas the ratiometric of normalized eTag2/eTag1 signal (shown in Figs. 11Band 11D).

Example 8: Shc/Her-3 Receptor-Adaptor Interaction

In this example, an assays were designed as shown in Figs. 12A and 12C.In Fig. 12A, Her2 receptor (1200) and Her3 receptor (1202) form a dimerin cell surface membrane (1204) and each receptor is represented ashaving phosphorylated sites (1209 and 1210). Shc proteins (1206 and1208) bind to phosphylation sites (1210) and (1209), respectively. Afirst binding compound (1214) and cleaving probe (1216) are specific fordifferent antigenic determinants of the extracellular domain of Her2receptor (1200). A second binding compound (1212) is specific for Shcproteins (1206 and 1208). The assay designs of Figs. 12A and 12C aresimilar, except that in the design of Fig. 12A the cleaving probe isspecific for the Her2 receptor, and in the design of Fig. 12C, thecleaving probe is specific for the Her3 receptor. Thus, in the formercase, total Her2 receptor is measured, whereas in the latter case totalHer3 receptor is measured. The assays were carried out as follows.Sample preparation was carried out as above (Example 7).

Assay design: Receptor complex formation is quantified ratiometricallybased on the schematics illustrated in each figure. That is, in Figs.12B and 12D the readout of the assays are the peak ratios of mT₂/mT₁ asa function of HRG concentration.

The total assay volume is 40 ul. The lysate volume is adjusted to 10 ulwith lysis buffer. The antibodies are diluted in lysis buffer up to 20ul. Typically about 5000 to 500,000 cell-equivalent of lysates is usedper reaction.

Procedure: Working concentrations of pre-mixed antibodies prior toadding into reaction: For Her-3/Shc complex with cleaving probe at Her-3(the design of Fig. 12B): eTag1_anti-Her-3 at 10 nM (eTag1 was Pro14 inthis assay) eTag2_anti-Shc at 10 nM (eTag2 was Pro12 in this assay)eTag3_anti-phospho-Tyr at 10 nM (eTag3 was Pro2 in this assay)Biotin_anti-Her-3 at 20 nM Universal Standard US-1 at 700 nM ForHer-2/Shc complex with cleaving probe at Her-2 (the design of 12A):eTag1_anti-Her-2 at 10 nM (eTag1 was Pro14 in this assay) eTag2_anti-Shcat 10 nM (eTag2 was Pro12 in this assay) eTag3_anti-phospho-Tyr at 10 nM(eTag3 was Pro2 in this assay) Biotin_anti-Her-2 at 20 nM UniversalStandard US-1 at 700 nM 1. To assay 96-well filter plate (MilliporeMAGVN2250), add 20 ul antibody mix to 10 ul lysate and incubate for 1hour at 4 degrees C. 2. Add 10 ul streptavidin-derivatized cleavingprobe (final 4 ug/well) to assay well and incubate for 40 min. 3. Add200 ul wash buffer and apply vacuum to empty. 4. Add 30 ul illuminationbuffer and illuminate. 5. Transfer 10 ul of each reaction to CE assayplate for analysis.

Data Analysis: 1. Normalize relative fluorescence units (RFU) signal ofeach molecular tag against that of internal Universal Standard US-1. 2.Subtract RFU of “no lysate” background control from correspondingnormalized signals for molecular tags. 3. Report receptor complexformation as the ratiometric of normalized mT₂/mT₁ signals (shown inFigs. 12B and 12D) and receptor phosphorylation (data not shown) asmT3/mT1 signals.

Example 9: Correlation Between Her2-Her3 Heterodimer Measurements andHer3-PI3K Complex Measurements in Breast Tumor Samples

In this example, human breast tumor samples were separately assayedusing the methods described above to determine the amounts of Her2-Her3heterodimers and the amounts of Her3-PI3K complex. Fig. 13 illustratesdata obtained from such assays, which shows that the two measurementsare correlated.

Example 10: Expression of Her1-Her2 and Her2-Her3 Heterodimers in BreastTumor Tissue Lysates and Normal Tissue Lysates

Frozen human breast tumor tissue samples and normal tissue samples wereobtained from the William Bainbridge Genomic Foundation (BainbridgeIsland, WA). Assays having a format as shown in Fig. 3E were performedon 32 tumor tissue samples and 30 normal tissue samples. Tumor tissuesconsisted of a mixture of tumor and normal cells that varied from about25 percent to over 90 percent according to pathology data supplied withthe tissues by the vendor. Samples were prepared and the assays carriedout essentially as described for Examples 2 and 6. Data is reported aspeak area or intensity of the separated molecular tag released from thebinding compound specifically bound to the receptor opposite thecleaving probe, i.e. the molecular tag corresponding to “mT₁” in Fig.3E. No attempt was made to normalize the signals generated according topercentage tumor cells in a sample.

The data from these measurements are shown in Fig. 14A (Her1-Her2heterodimer measurements) and Fig. 14B (Her2-Her3 heterodimermeasurements), where the open squares indicate measurements on tumortissues and the solid diamonds indicate measurements on normal tissues.The data show that tumor cells in substantial fractions of the tumortissue samples express large amounts of Her1-Her2 heterodimers andHer2-Her3 heterodimers relative to those expressed in the cells of thenormal tissue samples.

Example 11: Measurement of Receptor Dimers in Formalin Fixed ParaffinEmbedded Tissue Samples

In this example, model fixed tissues made from pelleted cell lines wereassayed for the presence of Her receptor dimers. The assay design forheterodimers was essentially the same as that described in Fig. 4A, withexceptions as noted below. That is, four components are employed: (i) acleaving probe comprising a biotinylated monoclonal antibody conjugatedto a cleavage-inducing moiety (in this example, aphotosensitizer-derivatized streptavidin, as illustrated in Fig. 3E) andspecific for one of the receptors of the dimer, (ii) a monoclonalantibody derivatized with a first molecular tag and specific for thesame receptor as the cleaving probe, (iii) a monoclonal antibodyderivatized with a second molecular tag and specific for the receptoropposite to that the cleaving probe is specific for, and (iv) amonoclonal antibody derivatized with a third molecular tag and specificfor an intracellular phosphorylated tyrosine. The assay design forhomodimers was essentially the same as that described in Fig. 1D, withexceptions as noted below.

In each case, model fixed tissues were prepared as follows: cells grownon tissue culture plates were stimulated with either EGF or HRG asdescribed in the prior examples, after which they were washed andremoved by scrapping. The removed cells were centrifuged to form apellet, after which formalin was added and the mixture was incubatedovernight at 4 degrees C. The fixed pellet was embedded in paraffinusing a Miles Tissue Tek III Embedding Center, after which 10 um tissuesections were sliced from the pellet using a microtome (Leica model2145). Tissue sections were placed on positively charged glassmicroscope slides (usually multiple tissue sections per slide) and bakedfor 1 hr at 60 degrees C.

Tissue sections on the slides were assayed as follows: Tissue sectionson a slide were de-waxed with EZ-Dewax reagent (Biogenex, San Ramon, CA)using the manufacturer’s recommended protocol. Briefly, 500 uL EZ-Dewaxwas added to each tissue section and the sections were incubated at RTfor 5 min, after which the slide was washed with 70% EtOH. This step wasrepeated and the slide was finally rinsed with deionized water, afterwhich the slide was incubated in water at RT for 20 min. The slide wasthen immersed into a 1X Antigen Retrieval solution (Biogenesis,Brentwood, NH) at pH 10, after which it was heated for 15 min in amicrowave oven (5 min at high power setting followed by 10 min at a lowpower setting). After cooling to RT (about 45 min), the slide was placedin a water bath for 5 min, then dried. Tissue sections on the driedslide were circled with a hydrophobic wax pen to create regions capableof containing reagents placed on the tissue sections (as illustrated inFigs. 1H-1I), after which the slide was washed three times in 1XPerm/Wash (BD Biosciences). To each section 50-100 uL blocking bufferwas added, and the slide was placed in a covered humidified boxcontaining deionized water for 2 hr at 4 degrees C, after which theblocking buffer was removed from each section by suction. (Blockingbuffer is 1X Perm/Wash solution with protease inhibitors (Roche),phosphatase inhibitors (sodium floride, sodium vanadate, beta-glycerolphosphate), and 10% mouse serum). To each section 40-50 uL of antibodymix containing binding compounds and cleaving probe was added (each at 5ug/mL, except that biotin-Ab5 (anti-Her1) was at 10 ug/mL in theHer1-Her2 assay), and the slide was placed in a humidified box overnightat 4 degrees C. The sections were then washed three times with 100 uLPerm/Wash containing protease and phosphatase inhibitors, after which 50uL of photosensitizer in 1X Perm/Wash solution (containing protease andphosphatase inhibitors) was added. The slide was then incubated for1-1.5 hr at 4 degrees C in the dark in a humidified box, after which thephotosensitizer was removed by suction while keeping the slide in thedark. While remaining in the dark, the slide was then immersed in .01XPBS and incubated on ice for 1 hr. The slide was remove from the PBS,dried, and to each section, 40-50 uL 0.01X PBS with 2 pM fluorescein wasadded, after which it was illuminated with a high power laser diode(GaAIAs IR emitter, model OD-880W, OPTO DIODE CORP, Newbury Park, CA)for 1 hr. The fluorescein acts as a standard to assist in correlatingpeaks in an electropherogram with moleuclar tags. After illumination,the solution covering each tissue section was mixed by gentle pipetingand transferred to a CE plate for analysis on an Applied Biosystems(Foster City, CA) model 3100 capillary electrophoresis instrument.

Fig. 15A shows data from analysis of Her1-Her1 homodimers and receptorphosphorylation in sections from fixed pellets of breast adenocarcinomacell line, MDA-MB-468 (ATCC accession no. HTB-132), prepared from eithernon-stimulated cells or cells stimulated with 100 nM EGF. Biotinylatedanti-Her1 monoclonal antibody (Labvision) at 2 ug/mL was use as theprimary antibody of the cleaving probe (for cleavage methylene-bluederivatized streptavidin (described above) was attached through thebiotin). Pro10-derivatized anti-Her1 monoclonal antibody (Labvision) at2 ug/mL was used to measure homodimerized Her1. Pro1-derivatizedanti-Her1 monoclonal antibody (Labvision) at 0.8 ug/mL was used tomeasure total Her1. Unlabeled antibody Ab-5 was also included in thereactions at 3.2 ug/mL. Pro2-derivatized monoclonal antibody(anti-phosphorylated-Tyr, Cell Signaling) at 0.5 ug/mL was used tomeasure intracellular phosphorylation. The data from fixed tissuemeasurements confirm and are consistent with measurements on celllysates that show increases in Her1-Her1 homodimer expression andintracellular phosphoryation due to EGF stimulation.

Fig. 15B shows data from analysis of Her2-Her2 homodimers and receptorphosphorylation in sections from fixed pellets of breast cancer celllines MCF-7 and SKBR-3. All monoclonal antibodies used as cleavingprobes or binding compounds were used at concentrations of 5 ug/mL. Inorder to generate better cleavage, in this assay two cleaving probeswere employed, one directed to an extracellular antigenic determinant ofHer2 and one directed to an intracellular antigenic determinant of Her2.The data from fixed tissue measurements confirm that SKBR3 cells expresshigher levels of Her2-Her2 homodimers than MCF-7 cells.

Fig. 15C shows data from analysis of Her1-Her2 heterodimers and receptorphosphorylation in sections from fixed pellets of breast adenocarcinomacell line, MCF-7, prepared from either non-stimulated cells or cellsstimulated with 40 nM EGF. Two cleaving probes were employed onecomprising anti-Her1 monoclonal antibody (at 5 ug/mL) and the othercomprising anti-Her1 monoclonal antibody (at 10 ug/mL) (both fromLabvision) in order to increase the rate at which molecular tags werereleased. The data show that increases in Her1-Her2 heterodimerexpression due to EGF stimulation is detected in fixed tissue.

Fig. 15D shows data from analysis of Her1-Her2 heterodimers and receptorphosphorylation in sections from fixed pellets of breast adenocarcinomacell line, 22Rv1, prepared from either non-stimulated cells or cellsstimulated with 100 nM EGF. Again, measurements on fixed tissuesdemonstrates the up-regulation of Her1-Her2 dimers and Her receptorphosphorylation in response to treatment with EGF.

Fig. 15E shows data from analysis of Her2-Her3 heterodimers and receptorphosphorylation in sections from fixed pellets of breast adenocarcinomacell line, MCF-7, prepared from either non-stimulated cells or cellsstimulated with 40 nM HRG. In this example, binding reactions andcleavage reactions took place in tubes containing sections, rather thanmicroscope slides. Otherwise, the protocol was essentially the same asthat for detecting the Her1-Her2 dimers. The data show that increases inHer2-Her3 heterodimer expression due to HRG stimulation is detected infixed tissue.

Fig. 15F shows data from analysis of Her2-Her3 heterodimers andPI3K-Her3 dimers in sections from fixed pellets of MCF-7 cells eithernon-stimulated or stimulated with 40 nM HRG. The assay design forPI3K-Her3 was essentially as described in Fig. 11A. The above fixationprotocol was followed in both cases, except that neither sample wastreated with antigen retrieval reagents. The data show that Her2-Her3dimers increased with treatment by HRG, but that the amount of PI3K-Her3dimer remained essentially unchanged.

Fig 15G shows data from analysis of total PI3K, total Her2-Her3 dimer,and total Her3 all relative to amount of tubulin. Tubulin was measuredin a conventional sandwich-type assay employing a cleavage probe and abinding compound with a molecular tag. Tubulin was measured to testprocedures for normalizing dimer measurement against a targetrepresentative of total cell number in a sample, which may be requiredfor measurements on samples with heterogeneous cell types. The data showthat the ratios of PI3K-Her3 and Her2-Her3 to tubulin are qualitativelythe same as the measurements directly on PI3K-Her3 and Her2-Her3.

1.
 62. A method for detecting in a biological sample the presence oramount of a receptor complex comprising a Platelet Derived Growth Factorreceptor (PDGFR) and a second protein, comprising: (a) contacting withthe sample a binding compound having a molecular tag attached thereto bya cleavable linkage and a cleaving probe having a cleavageinducing-moiety with an effective proximity, wherein the bindingcompound specifically binds either the PDGFR or the second protein andthe cleaving probe specifically binds an opposite member of the receptorcomplex from that bound by the cleaving probe; (b) cleaving thecleavable linker of the binding compound within the effective proximityof the cleavage-inducing moiety of the cleaving probe, thereby releasingthe molecular tag; and (c) identifying the released molecular tag todetermine the presence or amount of the receptor complex comprising thePDGFR and the second protein in the sample.
 2. 63. The method of claim62, wherein the second protein is a cell surface receptor.
 3. 64. Themethod of claim 63, wherein the second protein is Her1.
 4. 65. Themethod of claim 63, wherein the second protein is Her2.
 5. 66. Themethod of claim 63, wherein the second protein is Her3.
 6. 67. Themethod of claim 62, wherein the binding compound comprises an anti-PDGFR antibody.
 7. 68. The method of claim 62, wherein the bindingcompound comprises an anti-Her1 antibody.
 8. 69. The method of claim 62,wherein the binding compound comprises an anti-Her2 antibody.
 9. 70. Themethod of claim 62, wherein the binding compound comprises an anti-Her3antibody.
 10. 71. The method of claim 62, wherein the cleaving probecomprises an anti- PDGFR antibody.
 11. 72. The method of claim 62,wherein the cleaving probe comprises an anti-Her1 antibody.
 12. 73. Themethod of claim 62, wherein the cleaving probe comprises an anti-Her2antibody.
 13. 74. The method of claim 62, wherein the cleaving probecomprises an anti-Her3 antibody.
 14. 75. The method of claim 62, whereinthe biological sample comprises cancer cells.
 15. 76. The method ofclaim 75, wherein the cancer cells are obtained from a patient.
 16. 77.The method of claim 76, wherein the biological sample is obtained by abiopsy of the cancer.
 17. 78. The method of claim 76, wherein thebiological sample is obtained by purifying circulating cancer cells fromthe patient's blood.
 18. 79. The method of claim 75, wherein the canceris a lung cancer.
 19. 80. The method of claim 75, wherein the cancer isa breast cancer.
 20. 81. The method of claim 62, wherein the step ofdetecting is preceded by electorphoretically separating the moleculartag.
 21. 82. The method of claim 62, wherein the cleavage-inducingmoiety is a photosensitizer.